Search results for "molecular model"
showing 10 items of 274 documents
Evaluation of the IKKβ Binding of Indicaxanthin by Induced-Fit Docking, Binding Pose Metadynamics, and Molecular Dynamics
2021
Background: Indicaxanthin, a betaxanthin belonging to the betalain class of compounds, has been recently demonstrated to exert significant antiproliferative effects inducing apoptosis of human melanoma cells through the inhibition of NF-κB as the predominant pathway. Specifically, Indicaxanthin inhibited IκBα degradation in A375 cells. In resting cells, NF-κB is arrested in the cytoplasm by binding to its inhibitor protein IκBα. Upon stimulation, IκBα is phosphorylated by the IKK complex, and degraded by the proteasome, liberating free NF-κB into the nucleus to initiate target gene transcription. Inhibition of the IKK complex leads to the arrest of the NF-κB pathway.Methods: To acquire deta…
Pentapeptides containing two dehydrophenylalanine residues - synthesis, structural studies and evaluation of their activity towards cathepsin C
2008
Synthesis, structural and biological studies of pentapeptides containing two Delta Phe residues (Z and E isomers) in position 2 and 4 in peptide chain were performed. All the investigated peptides adopted bent conformation and majority of them could exist as two different. conformers in solution. Only pentapeptides. containing free N-termini appeared to act as weak inhibitors of cathepsin C with the slow-binding, competitive mechanism of inhibition. free acids being bound slightly better than their methyl esters. Results of Molecular modeling suggested significant difference between peptides, depending of the type of amino acid residue in position 5 in peptide chain. Dehydropeptides contain…
Equation of State for Macromolecules of Variable Flexibility in Good Solvents: A Comparison of Techniques for Monte Carlo Simulations of Lattice Mode…
2007
The osmotic equation of state for the athermal bond fluctuation model on the simple cubic lattice is obtained from extensive Monte Carlo simulations. For short macromolecules (chain length N=20) we study the influence of various choices for the chain stiffness on the equation of state. Three techniques are applied and compared in order to critically assess their efficiency and accuracy: the repulsive wall method, the thermodynamic integration method (which rests on the feasibility of simulations in the grand canonical ensemble), and the recently advocated sedimentation equilibrium method, which records the density profile in an external (e.g. gravitation-like) field and infers, via a local …
Algebraic Treatment of a Three-Oscillator System: Applications to Some Molecular Models
1997
Abstract A new algebraic treatment of a three-oscillator system, called 3d formalism, is proposed. First, arbitrary tensor operators, expressed in terms of elementary creation and annihilation boson operators, are built within the standard algebraic chain u (3) ⊃ so (3) ⊃ so (2). Their matrix elements are next derived in a standard basis. Some applications, which require few adaptions or extensions, are proposed. They allow one to recover, for instance, Hecht's and tetrahedral Hamiltonians associated with threefold degenerate modes of spherical molecules and the vibron model Hamiltonian introduced for diatomic molecules.
Simple sampling Monte Carlo methods
2005
Single-cluster Monte Carlo study of the Ising model on two-dimensional random lattices.
1994
We use the single-cluster Monte Carlo update algorithm to simulate the Ising model on two-dimensional Poissonian random lattices with up to 80,000 sites which are linked together according to the Voronoi/Delaunay prescription. In one set of simulations we use reweighting techniques and finite-size scaling analysis to investigate the critical properties of the model in the very vicinity of the phase transition. In the other set of simulations we study the approach to criticality in the disordered phase, making use of improved estimators for measurements. From both sets of simulations we obtain clear evidence that the critical exponents agree with the exactly known exponents for regular latti…
Application of the Monte Carlo coherent-anomaly method to two-dimensional lattice-gas systems with further-neighbor interactions
1990
A Monte Carlo version of the coherent-anomaly method has been used to determine critical properties of a two-dimensional Ising ferromagnet with nearest- and next-nearest-neighbor interactions and of a series of two-dimensional lattice-gas systems of particles interacting via 6-12 Lennard-Jones potential. It has demonstrated that the method leads to quite accurate determination of critical temperature but is less successful when used to determine the values of critical exponents \ensuremath{\gamma} and \ensuremath{\nu}.
Monte Carlo simulation of correlated electrons in disordered systems
1992
Abstract The properties of many-electron states in disordered systems with long-range electron-eletron interaction are investigated by means of a Monte Carlo simulation. Using the Metropolis algorithm, three-dimensional systems up to 512 sites are systematically analysed. The low-lying excitations are investigated in order to distinguish between one-particle and many-particle hopping. In the interesting regime in which disorder and correlation effects are equally important we find that variable-range hopping is insignificant for electron transfer when compared with the contribution from nearest-neighbour one-electron hopping processes as well as variable-number hopping.
Quantum Monte Carlo methods
2005
Introduction In most of the discussion presented so far in this book, the quantum character of atoms and electrons has been ignored. The Ising spin models have been an exception, but since the Ising Hamiltonian is diagonal (in the absence of a transverse magnetic field), all energy eigenvalues are known and the Monte Carlo sampling can be carried out just as in the case of classical statistical mechanics. Furthermore, the physical properties are in accord with the third law of thermodynamics for Ising-type Hamiltonians (e.g. entropy S and specific heat vanish for temperature T → 0, etc.) in contrast to the other truly classical models dealt with in previous chapters (e.g. classical Heisenbe…
Monte Carlo Study of Diffusion Noise Reduction in GaAs Operating under Periodic Conditions
2009
The effects of an external correlated source of noise on the intrinsic carrier noise in a low‐doped GaAs bulk, operating under periodic conditions, are investigated. Numerical results confirm that the dynamical response of electrons driven by a high‐frequency periodic electric field receives a benefit by the constructive interplay between the fluctuating field and the intrinsic noise of the system. In particular, in this contribute we show a nonmonotonic behavior of the integrated spectral density, which value critically depends on the correlation time of the external noise source.