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1.
J Chem Phys ; 160(8)2024 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-38415832

RESUMO

A scaling law for the osmotic pressure of quasi-two-dimensional polymer melts as a function of concentration is obtained, which shows fractal characteristics. Structural properties such as the chains' contour length and their inner-monomer pair distribution function display fractal scaling properties as well. These predictions are confirmed with mesoscale numerical simulations. The chains are swollen and highly entangled, yet Flory's exponent is always ν = 1/2. The melt can be considered a fluid of "blobs" whose size becomes renormalized in terms of the contour's length while the fractal dimension df increases monotonically between 5/4 and 2, as the monomer concentration is increased. The semidilute scaling of the pressure is recovered when df = 1. Our results agree with recent experiments and with numerical reports on quasi-2d melts. This work provides a new paradigm to study and interpret thermodynamic and structural data in low-dimensional polymer melts, namely as fractal macromolecular objects.

2.
RSC Adv ; 10(23): 13405-13409, 2020 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-35493002

RESUMO

The compression force with indentation on a polymer brush with chains of unequal lengths is predicted with numerical simulations, as a function of increasing hardness of the grafting surface, finding that properties of the brush are distinguished from those of the surface and that its hardness propagates through the brush.

3.
J Mol Model ; 23(11): 306, 2017 Oct 06.
Artigo em Inglês | MEDLINE | ID: mdl-28986687

RESUMO

The interfacial tension between immiscible liquids is studied as a function of a model linear surfactant length and concentration using coarse-grained, dissipative particle dynamics numerical simulations. The adsorption isotherms obtained from the simulations are found to be in agreement with Langmuir's model. The reduction of the interfacial tension with increasing surfactant concentration is found to display some common characteristics for all the values of chain length modeled, with our predictions being in agreement with Szyszkowski's equation. Lastly, the critical micelle concentration is predicted for all surfactant lengths, finding exponentially decaying behavior, in agreement with Kleven's model. It is argued that these findings can be helpful guiding tools in the interpretation of available experiments and in the design of new ones with new surfactants and polymers.

4.
Biosystems ; 142-143: 52-67, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27020756

RESUMO

The phenomenon of protein folding is a fundamental issue in the field of the computational molecular biology. The protein folding inside the cells is performed in a highly inhomogeneous, tortuous, and correlated environment. Therefore, it is important to include in the theoretical studies the medium where the protein folding is developed. In this work we present the combination of three models to mimic the protein folding inside of an inhomogeneous medium. The models used here are Hydrophobic-Polar (HP) in 2D square arrangement, Evolutionary Algorithms (EA), and the Dual Site Bond Model (DSBM). The DSBM model is used to simulate the environment where the HP beads are folded; in this case the medium is correlated and is fractal-like. The analysis of five benchmark HP sequences shows that the inhomogeneous space provided with a given correlation length and fractal dimension plays an important role for correct folding of these sequences, which does not occur in a homogeneous space.


Assuntos
Simulação por Computador , Conformação Proteica , Dobramento de Proteína , Proteínas/química , Algoritmos , Sequência de Aminoácidos , Biologia Computacional/métodos , Fractais , Modelos Químicos , Modelos Moleculares , Reprodutibilidade dos Testes , Termodinâmica
5.
J Chem Phys ; 128(13): 134705, 2008 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-18397092

RESUMO

The extremely narrow production peak of N2 and CO2 which occurs in the reaction of NO+CO on Pt(100), a phenomenon known as "surface explosion," is studied using a dynamic Monte Carlo method on a square lattice at low pressure under isothermal conditions. This analysis incorporates recent experimental evidence obtained for the same reaction on a Rh(111) surface, which has shown that N2 production occurs either from the classical N+N recombination step or by the formation and successive decay of a (N-NO)* intermediary species. Moreover, the NO dissociation rate is inhibited by coadsorbed NO and CO molecules and is enhanced both by the presence of empty sites and adsorbed N atoms as nearest neighbors. These effects are taken into account in this study, along with the experimental adsorption, desorption, and diffusion rates of the reactants. The "explosive" phenomenon is analyzed through the evolution over time of an adsorbed NO+CO monolayer at a fixed temperature of 400 K. Furthermore, as the diffusion processes of the adsorbates are included, cellular structures are observed. Our simulations show quantitative agreement in the position of maxima with those obtained through experiments using isothermal desorption mass spectroscopy.

6.
J Phys Chem B ; 110(19): 9499-510, 2006 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-16686496

RESUMO

Oscillations and pattern formation driven by a surface reconstruction are studied for the catalytic reduction of NO by CO on Pt(100) single-crystal surfaces through dynamic Monte Carlo simulations at low pressure and relatively high temperatures conditions. This study incorporates recent experimental evidence obtained for the same reaction on a Rh(111) surface, which modifies the reaction scheme used in previous approaches. The main consequence of such experimental evidence is that the production of N(2) occurs through two parallel mechanisms: (a) the classical N + N recombination step; (b) the formation and subsequent decay of an (N-NO) intermediate species as the fastest pathway. Moreover, different factors influencing the NO dissociation rate, the key step in the whole reaction, such as the availability of neighboring vacant sites, the formation of N-islands, and the presence of other NO and CO adsorbed species in the neighborhood, are also taken into account and their effects discussed. Sustained, modulated, irregular, and damped oscillations are observed in our analysis as well as the formation of cellular structures and turbulent patterns. The effect and the importance of each elementary reaction step on the behavior of the system are discussed.

7.
J Chem Phys ; 122(14): 144705, 2005 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-15847551

RESUMO

Kinetic oscillations in the catalytic reduction of NO by CO on a reconstructing Pt(100) surface are simulated by using a dynamic Monte Carlo method. The simulation is based on the HS model and takes into account an alternative reaction mechanism arising from recent experimental findings for the catalytic reduction of No on Rh(111), which replaces the classical N+N recombination step by the formation of a (N-NO)(*) intermediary species for the production of molecular nitrogen. A synchronized mechanism and spatiotemporal patterns are observed during the oscillations. Oscillations are analyzed in terms of the controlling parameters involved in the reaction mechanism. Different values of these parameters lead to sustained, attenuated, and modulated oscillations.

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