Search results for "SIMULATION"
showing 10 items of 5095 documents
Vanilloid Derivatives as Tyrosinase Inhibitors Driven by Virtual Screening-Based QSAR Models
2010
A number of vanilloids have been tested as tyrosinase inhibitors using Ligand-Based Virtual Screening (LBVS) driven by QSAR (Quantitative Structure-Activity Relationship) models as the multi-agent classification system. A total of 81 models were used to screen this family. Then, a preliminary cluster analysis of the selected chemicals was carried out based on their bioactivity to detect possible similar substructural features among these compounds and the active database used in the QSAR model construction. The compounds identified were tested in vitro to corroborate the results obtained in silico. Among them, two chemicals, isovanillin (K(M) (app) = 1.08 mM) near to kojic acid (reference d…
Atom, atom-type, and total nonstochastic and stochastic quadratic fingerprints: a promising approach for modeling of antibacterial activity.
2005
The TOpological MOlecular COMputer Design (TOMOCOMD-CARDD) approach has been introduced for the classification and design of antimicrobial agents using computer-aided molecular design. For this propose, atom, atom-type, and total quadratic indices have been generalized to codify chemical structure information. In this sense, stochastic quadratic indices have been introduced for the description of the molecular structure. These stochastic fingerprints are based on a simple model for the intramolecular movement of all valence-bond electrons. In this work, a complete data set containing 1006 antimicrobial agents is collected and presented. Two structure-based antibacterial activity classificat…
Harmonization of QSAR Best Practices and Molecular Docking Provides an Efficient Virtual Screening Tool for Discovering New G-Quadruplex Ligands
2015
Telomeres and telomerase are key players in tumorogenesis. Among the various strategies proposed for telomerase inhibition or telomere uncapping, the stabilization of telomeric G-quadruplex (G4) structures is a very promising one. Additionally, G4 stabilizing ligands also act over tumors mediated by the alternative elongation of telomeres. Accordingly, the discovery of novel compounds able to act on telomeres and/or inhibit the telomerase enzyme by stabilizing DNA telomeric G4 structures as well as the development of approaches efficiently prioritizing such compounds constitute active areas of research in computational medicinal chemistry and anticancer drug discovery. In this direction, we…
Virtual darwinian drug design: QSAR inverse problem, virtual combinatorial chemistry, and computational screening.
2001
The generation of diversity and its further selection by an external system is a common mechanism for the evolution of the living species and for the current drug design methods. This assumption allows us to label the methods based on generation and selection of molecular diversity as "Darwinian" ones, and to distinguish them from the structure-based, structure-modulation approaches. An example of a Darwinian method is the inverse QSAR. It consists of the computational generation of candidate chemical structures and their selection according to a previously established QSAR model. New trends in the field of combinatorial chemical syntheses comprise the concepts of virtual combinatorial synt…
The Tensor Networks Anthology: Simulation techniques for many-body quantum lattice systems
2019
We present a compendium of numerical simulation techniques, based on tensor network methods, aiming to address problems of many-body quantum mechanics on a classical computer. The core setting of this anthology are lattice problems in low spatial dimension at finite size, a physical scenario where tensor network methods, both Density Matrix Renormalization Group and beyond, have long proven to be winning strategies. Here we explore in detail the numerical frameworks and methods employed to deal with low-dimension physical setups, from a computational physics perspective. We focus on symmetries and closed-system simulations in arbitrary boundary conditions, while discussing the numerical dat…
Searching for exceptional points and inspecting non-contractivity of trace distance in (anti-) PT -symmetric systems
2022
Non-Hermitian systems with parity-time ($\mathcal{PT}$) symmetry and anti-$\mathcal{PT}$ symmetry give rise to exceptional points (EPs) with intriguing properties related to, e.g., chiral transport and enhanced sensitivity, due to the coalescence of eigenvectors. In this paper, we propose a powerful and easily computable tool, based on the Hilbert-Schmidt speed (HSS), which does not require the diagonalization of the evolved density matrix, to detect exactly the EPs and hence the critical behavior of the (anti-)$\mathcal{PT}\!-$symmetric systems, especially high-dimensional ones. Our theoretical predictions, made without the need for modification of the Hilbert space, which is performed by …
Diagrammatic approach to quantum search
2014
We introduce a simple diagrammatic approach for estimating how a randomly walking quantum particle searches on a graph in continuous-time, which involves sketching small weighted graphs with self-loops and considering degenerate perturbation theory's effects on them. Using this method, we give the first example of degenerate perturbation theory solving search on a graph whose evolution occurs in a subspace whose dimension grows with $N$.
Spatial Search by Continuous-Time Quantum Walk with Multiple Marked Vertices
2015
In the typical spatial search problems solved by continuous-time quantum walk, changing the location of the marked vertices does not alter the search problem. In this paper, we consider search when this is no longer true. In particular, we analytically solve search on the "simplex of $K_M$ complete graphs" with all configurations of two marked vertices, two configurations of $M+1$ marked vertices, and two configurations of $2(M+1)$ marked vertices, showing that the location of the marked vertices can dramatically influence the required jumping rate of the quantum walk, such that using the wrong configuration's value can cause the search to fail. This sensitivity to the jumping rate is an is…
Electromagnetic lattice gauge invariance in two-dimensional discrete-time quantum walks
2018
International audience; Gauge invariance is one of the more important concepts in physics. We discuss this concept in connection with the unitary evolution of discrete-time quantum walks in one and two spatial dimensions, when they include the interaction with synthetic, external electromagnetic fields. One introduces this interaction as additional phases that play the role of gauge fields. Here, we present a way to incorporate those phases, which differs from previous works. Our proposal allows the discrete derivatives, that appear under a gauge transformation, to treat time and space on the same footing, in a way which is similar to standard lattice gauge theories. By considering two step…
Phase transition of light on complex quantum networks
2012
Recent advances in quantum optics and atomic physics allow for an unprecedented level of control over light-matter interactions, which can be exploited to investigate new physical phenomena. In this work we are interested in the role played by the topology of quantum networks describing coupled optical cavities and local atomic degrees of freedom. In particular, using a mean-field approximation, we study the phase diagram of the Jaynes-Cummings-Hubbard model on complex networks topologies, and we characterize the transition between a Mott-like phase of localized polaritons and a superfluid phase. We found that, for complex topologies, the phase diagram is non-trivial and well defined in the…