Shadow Energy Functionals and Potentials in Born-Oppenheimer Molecular Dynamics

In Born-Oppenheimer molecular dynamics (BOMD) simulations based on density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative self-consistent field optimization procedure, which in practice never is fully converged. The calculated energies and the forces are therefore only approximate, which may lead to an unphysical energy drift and instabilities. Here we discuss an alternative shadow BOMD approach that is based on a backward error analysis. Instead of calculating approximate solutions for an underlying exact regular BO potential, we do the opposite. Instead, we calculate the exact electron density, energies, and forces, but for an underlying approximate shadow BO potential. In this way the calculated forces are conservative with respect to the shadow potential and generate accurate molecular trajectories with long-term energy stability. We show how such shadow BO potentials can be constructed at different levels of accuracy as a function of the integration time step, dt, from the minimization of a sequence of systematically improvable, but approximate, shadow energy density functionals. For each functional there is a corresponding ground state BO potential. These pairs of shadow energy functionals and potentials are higher-level generalizations of the original "0th-level" shadow energy functionals and potentials used in extended Lagrangian BOMD [Eur. Phys. J. B vol. 94, 164 (2021)]. The proposed shadow energy functionals and potentials are useful only within this dynamical framework, where also the electronic degrees of freedom are propagated together with the atomic positions and velocities. The theory is general and can be applied to MD simulations using approximate DFT, Hartree-Fock or semi-empirical methods, as well as to coarse-grained flexible charge models.Comment: 16 pages, 3 figure

Eigenvector Centrality Distribution for Characterization of Protein Allosteric Pathways

Determining the principal energy pathways for allosteric communication in biomolecules, that occur as a result of thermal motion, remains challenging due to the intrinsic complexity of the systems involved. Graph theory provides an approach for making sense of such complexity, where allosteric proteins can be represented as networks of amino acids. In this work, we establish the eigenvector centrality metric in terms of the mutual information, as a mean of elucidating the allosteric mechanism that regulates the enzymatic activity of proteins. Moreover, we propose a strategy to characterize the range of the physical interactions that underlie the allosteric process. In particular, the well known enzyme, imidazol glycerol phosphate synthase (IGPS), is utilized to test the proposed methodology. The eigenvector centrality measurement successfully describes the allosteric pathways of IGPS, and allows to pinpoint key amino acids in terms of their relevance in the momentum transfer process. The resulting insight can be utilized for refining the control of IGPS activity, widening the scope for its engineering. Furthermore, we propose a new centrality metric quantifying the relevance of the surroundings of each residue. In addition, the proposed technique is validated against experimental solution NMR measurements yielding fully consistent results. Overall, the methodologies proposed in the present work constitute a powerful and cost effective strategy to gain insight on the allosteric mechanism of proteins

Matrix Diagonalization as a Board Game: Teaching an Eigensolver the Fastest Path to Solution

Matrix diagonalization is at the cornerstone of numerous fields of scientific computing. Diagonalizing a matrix to solve an eigenvalue problem requires a sequential path of iterations that eventually reaches a sufficiently converged and accurate solution for all the eigenvalues and eigenvectors. This typically translates into a high computational cost. Here we demonstrate how reinforcement learning, using the AlphaZero framework, can accelerate Jacobi matrix diagonalizations by viewing the selection of the fastest path to solution as a board game. To demonstrate the viability of our approach we apply the Jacobi diagonalization algorithm to symmetric Hamiltonian matrices that appear in quantum chemistry calculations. We find that a significant acceleration can often be achieved. Our findings highlight the opportunity to use machine learning as a promising tool to improve the performance of numerical linear algebra.Comment: 14 page

A Reappraisal of Lymphadenectomy in Common Gynecological Cancers

Objectives: Lymph node dissection (LND) in gynecological malignancies has always been a cornerstone in the diagnosis of metastasis, it is also considered an important prognostic factor, and a reliable guide to management strategies. However, its incidence of complications, namely lymphedema, vascular injuries and other lesions, has led to a reconsideration of its efficacy and a comparison of the role of systematic vs. sentinel lymph node (SLN) dissection. Mechanism: Review of the literature using keywords such as “lymph nodes”, “sentinel lymph nodes”, “morbidity and mortality”, “gynecological cancers”, “endometrial cancer”, “ovarian cancer”, and “cervical cancer”. Findings in Brief: In the case of endometrial cancer, several studies have investigated the efficacy of SLN compared with systematic LND. Most of the results demonstrated the efficacy of SLN dissection in endometrial cancer, with the added benefit of lower morbidity. In patients with ovarian cancer, the mainstay of treatment is debulking with optimal cytoreductive surgery. Recent studies have compared systematic lymphadenectomy to non-lymphadenectomy, with an additional advantage in the cases of lymphadenectomy. However, since its publication, the lymphadenectomy in ovarian cancers (LIONS) trial, has revolutionized the standard of care for patients with advanced ovarian cancer and has called into question the increased morbidity and mortality in systematic lymphadenectomy. In cervical cancers, lymph node status is considered to be the most important prognostic factor. In this case, limiting lymphadenectomy to the borders of the inferior mesenteric artery seems promising, and studies are currently being carried out to investigate the feasibility of SLN dissection instead of systematic lymph node dissection. Conclusions: SLN dissection is associated with lower morbidity and mortality, and has been shown to be superior to systematic lymphadenectomy in several studies. However, more research and specific guidelines are needed to better select either one or the other method in the management of gynecological cancers. Copyright: © 2023 The Author(s)

Genetic characterization of Carnivore Parvoviruses in Spanish wildlife reveals domestic dog and cat-related sequences

The impact of carnivore parvovirus infection on wild populations is not yet understood; disease signs are mainly developed in pups and assessing the health of litters in wild carnivores has big limitations. This study aims to shed light on the virus dynamics among wild carnivores thanks to the analysis of 213 samples collected between 1994 and 2013 in wild ecosystems from Spain. We determined the presence of carnivore parvovirus DNA by real‐time PCR and sequenced the vp2 gen from 22 positive samples to characterize the strains and to perform phylogenetic analysis. The presence of carnivore parvovirus DNA was confirmed in 18% of the samples, with a higher prevalence detected in wolves (Canis lupus signatus, 70%). Fourteen sequences belonging to nine wolves, three Eurasian badgers (Meles meles), a common genet (Genetta genetta) and a European wildcat (Felis silvestris) were classified as canine parvovirus 2c (CPV‐2c); five sequences from three wolves, a red fox (Vulpes vulpes) and a stone marten (Martes foina) as CPV‐2b; and three sequences from a badger, a genet and a stone marten as feline parvovirus (FPV). This was the first report of a wildcat infected with a canine strain. Sequences described in this study were identical or very close related to others previously found in domestic carnivores from distant countries, suggesting that cross‐species transmission takes place and that the parvovirus epidemiology in Spain, as elsewhere, could be influenced by global factors