Search results for "molecular model"
showing 10 items of 274 documents
DNA-Binding and Anticancer Activity of Pyrene-Imidazolium Derivatives
2016
DNA-binding investigations showed that two different derivatives endowed with pyrene and imidazolium moieties, 1 and 2, strongly bind both double-stranded DNA and telomeric sequences in G-quadruplex (G4) conformation. The values of the DNA-binding constants indicate that 1 and 2 show preferential affinity for G4-DNA, of about one and two orders of magnitude, respectively. Moreover, 1 and 2 inhibit short and long-term proliferation of breast cancer cell lines in a time- and dose-dependent fashion. Remarkably, senescence assays indicate that telomeric G4-DNA is a possible biotarget for the cytotoxic activity of 2. Molecular dynamics simulations suggest that the stronger binding of 2 with G4-D…
METHYLOMIC SIGNATURE AND MOLECULAR MODELLING TO BETTER UNDERSTAND AUTOPHAGY INDUCED BY PHYTOCHEMICAL IN CACO-2 CELLS
2019
The binomial “autophagy-cancer” is intricate and methylomic studies can help to understand it by changing point of view from a gene level to an -omic one. Recently, autophagy-modulating properties of several phytochemicals have attracted attention in anticancer research. We evaluated whether Indicaxanthin (IND), the peculiar known beneficial phytochemical of prickly pear, seasonally available in the southern Italy, could induce autophagy in Caco2 cells, and whether it results from an epigenomic modification and/or a direct molecular interaction. IND increased autophagy in Caco-2 cells; the methylomic signature, obtained by Reduced Representation Bisulfite Sequencing (15 million of clusters)…
Cross Correlations in Scaling Analyses of Phase Transitions
2008
Thermal or finite-size scaling analyses of importance sampling Monte Carlo time series in the vicinity of phase transition points often combine different estimates for the same quantity, such as a critical exponent, with the intent to reduce statistical fluctuations. We point out that the origin of such estimates in the same time series results in often pronounced cross-correlations which are usually ignored even in high-precision studies, generically leading to significant underestimation of statistical fluctuations. We suggest to use a simple extension of the conventional analysis taking correlation effects into account, which leads to improved estimators with often substantially reduced …
Cluster Monte Carlo algorithms
1990
Abstract The Swendsen-Wang and Wolff Monte Carlo algorithms are described in some detail, using the Potts model as an example. Various generalizations are then reviewed and some applications are discussed. Two complete Fortran programs for the algorithms are provided.
Monte Carlo study of asymmetric 2D XY model
1997
Employing the Polyakov-Susskind approximation in a field theoretical treatment, the t-J model for strongly correlated electrons in two dimensions has recently been shown to map effectively onto an asymmetric two-dimensional classical XY model. The critical temperature at which charge-spin separation occurs in the t-J model is determined by the location of the phase transitions of this effective model. Here we report results of Monte Carlo simulations which map out the complete phase diagram in the two-dimensional parameter space and also shed some light on the critical behaviour of the transitions.
N-Benzyl Residues as the P1′ Substituents in Phosphorus-Containing Extended Transition State Analog Inhibitors of Metalloaminopeptidases
2020
Peptidyl enzyme inhibitors containing an internal aminomethylphosphinic bond system (P(O)(OH)-CH2-NH) can be termed extended transition state analogs by similarity to the corresponding phosphonamidates (P(O)(OH)-NH). Phosphonamidate pseudopeptides are broadly recognized as competitive mechanism-based inhibitors of metalloenzymes, mainly hydrolases. Their practical use is, however, limited by hydrolytic instability, which is particularly restricting for dipeptide analogs. Extension of phosphonamidates by addition of the methylene group produces a P-C-N system fully resistant in water conditions. In the current work, we present a versatile synthetic approach to such modified dipeptides, based…
Bis- and Trisamides Derived From 1′-Aminoferrocene-1-carboxylic Acid and α-Amino Acids: Synthesis and Conformational Analysis
2009
Ferrocene derivatives with one or two achiral and chiral arms based on α-amino acids (Gly, l-Ala, l-Val) attached to the cyclopentadienyl rings were prepared by solution-phase peptide synthesis from N-acetyl- and N-Boc-protected 1′-aminoferrocene-1-carboxylic acids (Boc = tert-butoxycarbonyl). The conformational preference in the solid state of selected examples was elucidated by X-ray crystallography. The chiroptical properties of chiral bis- and trisamides were investigated by circular dichroism (CD) spectroscopy in solution. The conformational preference was studied by NMR and IR spectroscopy, as well as by molecular modeling (DFT). For the bisamides, a conformational library is observed…
Physics of the nuclear pore complex: Theory, modeling and experiment
2021
Abstract The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular “nanomachine” known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the…
Quantum Monte Carlo Simulations of Models Related to High-Tc Superconductivity on a Transputer Network
1991
Much of the insight into the low temperature behaviour of two-dimensional quantum antiferromagnets has been recently obtained by extensive Monte Carlo. These models are relevant in the study of the magnetic behaviour of high Tc compounds containing copper-oxide layers. While of little technical importance, the physical properties of these models are certainly important for the understanding of the new type of behaviour that leads to superconductivity under certain conditions.
Vectorized ‘‘TOPO’’ Program for the Theoretical Simulation of Molecular Shape
1991
The TOPO program for theoretical simulation of molecular shape is presented here. Molecular shape is characterized by a set of electrostatic and geometrical descriptors and topological indices including the fractal dimension of the accessible surface. An atom-atom analysis of all descriptors has been implemented. The program has been adapted for the realization of high-performance computing. Results are reported for porphine and phthalocyanine molecules.