Search results for "molecular modeling"
showing 10 items of 136 documents
On the adoption of the Monte Carlo method to solve one-dimensional steady state thermal diffusion problems for non-uniform solids
2013
Abstract The present paper is focussed on the investigation of the potential adoption of the Monte Carlo method to solve one-dimensional, steady state, thermal diffusion problems for continuous solids characterised by an isotropic, space-dependent conductivity tensor and subjected to non-uniform heat power deposition. To this purpose the steady state form of Fourier’s heat diffusion equation relevant to a continuous, heterogeneous and isotropic solid, undergoing a space-dependent heat power density has been solved in a closed analytical form for the general case of Cauchy’s boundary conditions. The thermal field obtained has been, then, put in a peculiar functional form, indicating that it …
Building large molecular models with plastic screw-on bottle caps and sturdy connectors
2016
An improved method of connecting atoms formed with screw-on bottle caps is described. Fishing line (artificial polymer), steel wire, and countersunk bolts with nyloc nuts are proposed as sturdy connectors. Advantages and disadvantages of each method are described. The molecular models are stable while handling, can be built in a relatively short time at low cost, and can be useful at every level of education. The method is an alternative to professional model kits, in particular in construction of large models for long-term usage.
Monte Carlo Simulation of Crystal-Liquid Phase Coexistence
2016
When a crystal nucleus is surrounded by coexisting fluid in a finite volume in thermal equilibrium, the thermodynamic properties of the fluid (density, pressure, chemical potential) are uniquely related to the surface excess free energy of the nucleus. Using a model for weakly attractive soft colloidal particles, it is shown that this surface excess free energy can be determined accurately from Monte Carlo simulations over a wide range of nucleus volumes, and the resulting nucleation barriers are completely independent from the size of the total volume of the system. A necessary ingredient of the analysis, the pressure at phase coexistence in the thermodynamic limit, is obtained from the in…
Spectroscopic characterization of non-covalent CuPc-GO system. Experiment and theory
2019
Abstract In this study we report on UV-vis, IR and Raman studies of non-covalent copper phthalocyanine (CuPc) – flake graphene oxide (GO) complex in water and in the solid phase. Experimental results were supported by molecular modeling of structure, electronic and vibrational parameters for free CuPc and its 1 : 1 complexes with water, benzene, phenol, neutral and deprotonated benzoic acid. HOMO-LUMO gaps for these complexes were calculated and compared with data derived from the absorption edge of Q-band in the recorded UV-vis spectra for free CuPc and its adduct with GO in water. Small but non-negligible changes in position of spectral bands observed as result of CuPc interaction with GO…
PET/PEN Blends of Industrial Interest as Barrier Materials. Part I. Many-Scale Molecular Modeling of PET/PEN Blends
2006
Mesoscale molecular simulations, based on parameters obtained through atomistic molecular dynamics and Monte Carlo calculations, have been used for modeling and predicting the behavior of PET/PEN blends. Different simulations have been performed in order to study and compare pure homopolymer blends with blends characterized by the presence of PET/PEN block copolymers acting as compatibilizer. A many-scale molecular modeling strategy was devised to evaluate PET/PEN blend characteristics, simulate phase segregation in pure PET/PEN blends, and demonstrate the improvement of miscibility due to the presence of the transesterification reaction products. The behavior of distribution densities and …
Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles
2020
Abstract The shape and size of self‐assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long‐range interactions. Combining small‐angle X‐ray/neutron scattering data, theoretical modelling, and computer simulations, sodium dodecyl sulfate (SDS), over a broad range of concentrations and ionic strengths, was investigated. Computer simulations indicate that micellar shape changes are associated with different binding of the counterions. By employing a toy model based on point charges on a surface, and comparing it to experiments and simulations, it is demonstrated that the observed morphological changes are caused by symmetry br…
A new strategy for effective learning in population Monte Carlo sampling
2016
In this work, we focus on advancing the theory and practice of a class of Monte Carlo methods, population Monte Carlo (PMC) sampling, for dealing with inference problems with static parameters. We devise a new method for efficient adaptive learning from past samples and weights to construct improved proposal functions. It is based on assuming that, at each iteration, there is an intermediate target and that this target is gradually getting closer to the true one. Computer simulations show and confirm the improvement of the proposed strategy compared to the traditional PMC method on a simple considered scenario.
Monte Carlo tests of theoretical predictions for critical phenomena: still a problem?
2000
Two Monte Carlo studies of critical behavior in ferromagnetic Ising models are described: the first one deals with the crossover from the Ising class to the mean field class, when the interaction range increases. The second study deals with the finite size behavior at dimensionalities above the marginal dimension where Landau theory applies. The numerical results are compared to pertinent theoretical predictions, and unsolved problems are briefly described.
What is the form of muscimol from fly agaric mushroom (Amanita muscaria) in water? An insight from NMR experiment supported by molecular modeling.
2020
ARTYKUŁ Z BADAŃ SPECJALNYCH
Phosphonic Acid Analogs of Fluorophenylalanines as Inhibitors of Human and Porcine Aminopeptidases N: Validation of the Importance of the Substitutio…
2020
International audience; A library of phosphonic acid analogs of phenylalanine substituted with fluorine, chlorine and trifluoromethyl moieties on the aromatic ring was synthesized and evaluated for inhibitory activity against human (hAPN) and porcine (pAPN) aminopeptidases. Fluorogenic screening indicated that these analogs are micromolar or submicromolar inhibitors, both enzymes being more active against hAPN. In order to better understand the mode of the action of the most active compounds, molecular modeling was used. It confirmed that aminophosphonic portion of the enzyme is bound nearly identically in the case of all the studied compounds, whereas the difference in activity results fro…