Biomedical subjects

Claudia Filippi

Publications and source records attributed to Claudia Filippi.

6 recordsLinked to original sources

PubMed2005

Diffusion Monte Carlo method with lattice regularization.

We introduce an efficient lattice regularization scheme for quantum Monte Carlo calculations of realistic electronic systems. The kinetic term is discretized by a finite difference Laplacian with two mesh sizes, a and a', chosen so that the electrons can diffuse in a configuration space which is in practice indistinguishable from the continuum, and the different length scales in the system can be efficiently taken in account. The regularized Hamiltonian goes to the continuous limit for a --> 0 and allows the inclusion of nonlocal potentials in a consistent variational scheme, substantially improving the accuracy upon previous nonvariational approaches.

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PubMed2005

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 NO2 and decapentaene (C10H12) molecules. The basic idea is to add terms to the straightforward expression for the Hessian of the energy that have zero expectation value, 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.

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PubMed2004

Excitations in photoactive molecules from quantum Monte Carlo.

Despite significant advances in electronic structure methods for the treatment of excited states, attaining an accurate description of the photoinduced processes in photoactive biomolecules is proving very difficult. For the prototypical photosensitive molecules, formaldimine, formaldehyde, and a minimal protonated Schiff base model of the retinal chromophore, we investigate the performance of various approaches generally considered promising for the computation of excited potential energy surfaces. We show that quantum Monte Carlo can accurately estimate the excitation energies of the studied systems if one constructs carefully the trial wave function, including in most cases the reoptimization of its determinantal part within quantum Monte Carlo. While time-dependent density functional theory and quantum Monte Carlo are generally in reasonable agreement, they yield a qualitatively different description of the isomerization of the Schiff base model. Finally, we find that the restricted open shell Kohn-Sham method is at variance with quantum Monte Carlo in estimating the lowest-singlet excited state potential energy surface for low-symmetry molecular structures.

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PubMed2004

Optimized Jastrow-Slater wave functions for ground and excited states: application to the lowest states of ethene.

A quantum Monte Carlo method is presented for determining multideterminantal Jastrow-Slater wave functions for which the energy is stationary with respect to the simultaneous optimization of orbitals and configuration interaction coefficients. The approach is within the framework of the so-called energy fluctuation potential method which minimizes the energy in an iterative fashion based on Monte Carlo sampling and a fitting of the local energy fluctuations. The optimization of the orbitals is combined with the optimization of the configuration interaction coefficients through the use of additional single excitations to a set of external orbitals. A new set of orbitals is then obtained from the natural orbitals of this enlarged configuration interaction expansion. For excited states, the approach is extended to treat the average of several states within the same irreducible representation of the pointgroup of the molecule. The relationship of our optimization method with the stochastic reconfiguration technique by Sorella et al. is examined. Finally, the performance of our approach is illustrated with the lowest states of ethene, in particular with the difficult case of the 1(1)B(1u) state.

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PubMed2003

Rituximab in idiopathic membranous nephropathy: a one-year prospective study.

Currently available monoclonal antibodies against the B cell surface antigen CD20 have been employed to explore whether specific inhibition of B cells may help improve the outcome of idiopathic membranous nephropathy (IMN) and may avoid the side effects of steroids and immunosuppressants. This prospective, observational study evaluated the 1-yr outcome of eight IMN patients with persistent (>6 mo) urinary protein excretion > 3.5 g/24 h given four weekly infusions of the anti-CD20 antibody rituximab (375 mg/m(2)). At 3 and 12 mo, proteinuria significantly decreased from mean (+/- SD) 8.6 +/- 4.2 to 4.3 +/- 3.3 (-51%, P < 0.005) and 3.0 +/- 2.5 (-66%, P < 0.005) g/24 h, albumin fractional clearance from 2.3 +/- 2.1 to 1.2 +/- 1.7 (-47%, P < 0.05) and 0.5 +/- 0.6 (-76%, P < 0.003), and serum albumin concentration increased from 2.7 +/- 0.5 to 3.1 +/- 0.3 (+21%, P < 0.05) and 3.5 +/- 0.4 (+41%, P < 0.05) mg/dl. At 12 mo, proteinuria decreased to < or =0.5 g/24 h or < or =3.5 g/24 h in two and three patients, respectively. Proteinuria decreased in the remaining patients by 74%, 44%, and 41%, respectively. Body weight, diastolic BP, and serum cholesterol progressively decreased in parallel with an improvement of edema in all patients. Renal function stabilized (Delta1/creatinine: +0.002 +/- 0.007). CD20 B lymphocytes fell below normal ranges up to study-end. No patient had major drug-related events or major changes in other laboratory parameters. Rituximab thus promotes sustained disease remission in patients otherwise predicted to progress to ESRD, and it is safe. The long-term risk/benefit profile of this novel, disease-specific approach seems much more favorable to that of commonly employed immunosuppressive drugs.

Adult↗

PubMed2002

Quantum Monte Carlo calculations of H2 dissociation on Si(001).

The dissociative adsorption of H2 on the Si(001) surface is theoretically investigated for several reaction pathways using quantum Monte Carlo methods. Our reaction energies and barriers are at large variance with those obtained with commonly used approximate exchange-correlation density functionals. Our results for adsorption support recent experimental findings, while, for desorption, the calculations give barriers in excess of the presently accepted experimental value, pinpointing the role of coverage effects and desorption from steps.

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