Search results for " molecular modeling"
showing 10 items of 76 documents
Critical phenomena without “hyper scaling”: How is the finite-size scaling analysis of Monte Carlo data affected?
2010
Abstract The finite size scaling analysis of Monte Carlo data is discussed for two models for which hyperscaling is violated: (i) the random field Ising model (using a model for a colloid-polymer mixture in a random matrix as a representative) (ii) The Ising bi-pyramid in computing surface fields.
Path-integral Monte Carlo study of crystalline Lennard-Jones systems.
1995
The capability of the path-integral Monte Carlo (PIMC) method to describe thermodynamic and structural properties of solids at low temperatures is studied in detail, considering the noble-gas crystals as examples. In order to reduce the systematic limitations due to finite Trotter number and finite particle number we propose a combined Trotter and finite-size scaling. As a special application of the PIMC method we investigate $^{40}\mathrm{Ar}$ at constant volume and in the harmonic approximation. Furthermore, isotope effects in the lattice constant of $^{20}\mathrm{Ne}$ and $^{22}\mathrm{Ne}$ are computed at zero pressure. The obtained results are compared with classical Monte Carlo result…
Cluster Expansions and Variational Monte Carlo in Medium Light Nuclei
1993
The B1 Brink-Boeker effective interaction is used to compute variational upper bounds for the ground state energy of nuclei from 16 O up to 40 Ca. The calculations are carried out by means of the Variational Monte Carlo method and with a multiplicative cluster expansion up to fourth order.
Path integral Monte Carlo study of the internal quantum state dynamics of a generic model fluid
1996
We study the quantum dynamics of a generic model fluid with internal quantum states and classical translational degrees of freedom in two spatial dimensions. The path integral Monte Carlo data for the imaginary time correlation functions are presented and analyzed by the maximum entropy method. A comparison of the frequency distribution with those of a mean field approximation and virial expansion shows good agreement at high and low densities, respectively. \textcopyright{} 1996 The American Physical Society.
Molecular-Level Characterization of Heterogeneous Catalytic Systems by Algorithmic Time Dependent Monte Carlo
2009
Monte Carlo algorithms and codes, used to study heterogeneous catalytic systems in the frame of the computational section of the NANOCAT project, are presented along with some exemplifying applications and results. In particular, time dependent Monte Carlo methods supported by high level quantum chemical information employed in the field of heterogeneous catalysis are focused. Technical details of the present algorithmic Monte Carlo development as well as possible evolution aimed at a deeper interrelationship of quantum and stochastic methods are discussed, pointing to two different aspects: the thermal-effect involvement and the three-dimensional catalytic matrix simulation. As topical app…
Development of novel dipeptide-like rhodesain inhibitors containing the 3-bromoisoxazoline warhead in a constrained conformation.
2015
Novel dipeptide-like rhodesain inhibitors containing the 3-bromoisoxazoline warhead in a constrained conformation were developed; some of them possess K(i) values in the micromolar range. We studied the structure-activity relationship of these derivatives and we performed docking studies, which allowed us to find out the key interactions established by the inhibitors with the target enzyme. Biological results indicate that the nature of the P2 and P3 substituents and their binding to the S2/S3 pockets is strictly interdependent.
Conformational Analysis of beta-Lactam-Containing Ferrocene Peptides
2009
The homochiral 3-amino-1-(4-methoxyphenyl)-4-phenyl-beta-lactam (≡ Alm) was conjugated with Boc-Ala giving Ala-Alm (9) after Boc-deprotection (Boc = tert-butoxycarbonyl, Ala = alanine). Coupling of FcCOOH (1) and Boc-Fca (10) with “ dipeptide” 9 resulted in the formation of FcCO-Ala-Alm (12) and the trisamide Boc-Fca-Ala-Alm (13), respectively (Fc = ferrocenyl, Fca = 1’ -aminoferrocene-1-carboxylic acid). The reactions were accomplished by the HOBt/EDC procedure and the products were obtained in good yields (HOBt = 1-hydroxybenzotriazole, EDC = N-(3-dimethylaminopropyl)-N’ -ethylcarbodiimide hydrochloride). Symmetrically 1, 1’ -disubstituted “ tetrapeptide” Fn(CO-Ala-Alm)2 (14) was prepared…
Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates.
1994
Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted…
Guide to Practical Work with the Monte Carlo Method
2002
The guide is structured such that we proceed from the “easy” simulation methods and algorithms to the more sophisticated. For each method the algorithms are presented by the technique of stepwise refinement. We first present the idea and the basic outline. From then on we proceed by breaking up the larger logical and algorithmic structures into smaller ones, until we have reached the level of single basic statements. Sometimes we may elect not to go to such a depth and the reader is asked to fill in the gaps.
Indicaxanthin from Opuntia ficus-indica Crosses the Blood–Brain Barrier and Modulates Neuronal Bioelectric Activity in Rat Hippocampus at Dietary-Con…
2015
Indicaxanthin is a bioactive and bioavailable betalain pigment from the Opuntia ficus-indica fruits. In this in vivo study, kinetic measurements showed that indicaxanthin is revealed in the rat brain within 1 h from oral administration of 2 μmol/ kg, an amount compatible with a dietary consumption of cactus pear fruits in humans. A peak (20 ± 2.4 ng of indicaxanthin per whole brain) was measured after 2.5 h; thereafter the molecule disappeared with first order kinetics within 4 h. The potential of indicaxanthin to affect neural activities was in vivo investigated by a microiontophoretic approach. Indicaxanthin, administered in a range between 0.085 ng and 0.34 ng per neuron, dose-dependentl…