Sofia Calero

Bio: Sofia Calero is an academic researcher from Pablo de Olavide University. The author has contributed to research in topics: Adsorption & Metal-organic framework. The author has an hindex of 49, co-authored 216 publications receiving 7673 citations. Previous affiliations of Sofia Calero include École Normale Supérieure & Complutense University of Madrid.

RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials

Abstract: A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License.

United Atom Force Field for Alkanes in Nanoporous Materials

Abstract: A novel united atom force field affords accurate and quantitative reproduction of the adsorption properties of linear and branched alkanes in nanoporous framework structures. The force field was generated by adjusting the parameters so as to faithfully reproduce the experimentally determined isotherms (particularly the inflection points) on MFI-type zeolite over a wide range of pressures and temperatures. It reproduces extremely well the Henry coefficients, heats of adsorption, preexponential factors, entropies of adsorption, and maximum loading. It is shown that the extension of the force field from MFI to other nanoporous framework topologies is successful, that it affords the prediction of topology-specific adsorption properties, and that it can be an effective tool to resolve the many discrepancies among experimental data sets.

Understanding the role of sodium during adsorption: a force field for alkanes in sodium-exchanged faujasites.

Abstract: We have developed a united atom force field able to accurately describe the adsorption properties of linear alkanes in the sodium form of FAU-type zeolites. This force field successfully reproduces experimental adsorption properties of n-alkanes over a wide range of sodium cation densities, temperatures, and pressures. The force field reproduces the sodium positions in dehydrated FAU-type zeolites known from crystallography, and it predicts how the sodium cations redistribute when n-alkanes adsorb. The cations in the sodalite cages are significantly more sensitive to the n-alkane loading than those in the supercages. We provide a simple expression that adequately describes the n-alkane Henry coefficient and adsorption enthalpy as a function of sodium density and temperature at low coverage. This expression affords an adequate substitute for complex configurational-bias Monte Carlo simulations. The applicability of the force field is by no means limited to low pressure and pure adsorbates, for it also successfully reproduces the adsorption from binary mixtures at high pressure.

Transferable Force Field for Carbon Dioxide Adsorption in Zeolites

Abstract: We have developed a complete force field that accurately reproduces the adsorption properties of carbon dioxide in a variety of zeolites with different topologies and compositions. The force field parameters were obtained by fitting to our own experimental data and validated with available data taken from the literature. The novelty of this force field is that it is fully transferable between different zeolite framework types, and therefore, it is applicable to all possible Si/Al ratios (with sodium as extra-framework cation) and for the first time affording the prediction of topology-specific and chemical composition-specific adsorption properties.

Computing the Heat of Adsorption using Molecular Simulations: The Effect of Strong Coulombic Interactions

Abstract: Molecular simulations are an important tool for the study of adsorption of hydrocarbons in nanoporous materials such as zeolites. The heat of adsorption is an important thermodynamic quantity that can be measured both in experiments and molecular simulations, and therefore it is often used to investigate the quality of a force field for a certain guest-host (g - h) system. In molecular simulations, the heat of adsorption in zeolites is often computed using either of the following methods: (1) using the Clausius-Clapeyron equation, which requires the partial derivative of the pressure with respect to temperature at constant loading, (2) using the energy difference between the host with and without a single guest molecule present, and (3) from energy/particle fluctuations in the grand-canonical ensemble. To calculate the heat of adsorption from experiments (besides direct calorimetry), only the first method is usually applicable. Although the computation of the heat of adsorption is straightforward for all-silica zeolites, severe difficulties arise when applying the conventional methods to systems with nonframework cations present. The reason for this is that these nonframework cations have very strong Coulombic interactions with the zeolite. We will present an alternative method based on biased interactions of guest molecules that suffers less from these difficulties. This method requires only a single simulation of the host structure. In addition, we will review some of the other important issues concerning the handling of these strong Coulombic interactions in simulating the adsorption of guest molecules. It turns out that the recently proposed Wolf method ( J. Chem. Phys. 1999, 110 , 8254 ) performs poorly for zeolites as a large cutoff radius is needed for convergence.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。