Marcia C. Barbosa

Bio: Marcia C. Barbosa is an academic researcher from Universidade Federal do Rio Grande do Sul. The author has contributed to research in topics: Phase transition & Diffusion (business). The author has an hindex of 39, co-authored 230 publications receiving 4640 citations. Previous affiliations of Marcia C. Barbosa include University of California, Santa Barbara & Federal University of Rio Grande do Norte.

Thermodynamic and dynamic anomalies for a three-dimensional isotropic core-softened potential.

Abstract: Using molecular-dynamics simulations and integral equations (Rogers-Young, Percus-Yevick, and hypernetted chain closures) we investigate the thermodynamics of particles interacting with continuous core-softened intermolecular potential. Dynamic properties are also analyzed by the simulations. We show that, for a chosen shape of the potential, the density, at constant pressure, has a maximum for a certain temperature. The line of temperatures of maximum density (TMD) was determined in the pressure-temperature phase diagram. Similarly the diffusion constant at a constant temperature, D, has a maximum at a density ρmax and a minimum at a density ρmin<ρmax. In the pressure-temperature phase diagram the line of extrema in diffusivity is outside of the TMD line. Although this interparticle potential lacks directionality, this is the same behavior observed in simple point charge/extended water.

Static and dynamic properties of stretched water

Abstract: We present the results of molecular dynamics simulations of the extended simple point charge model of water to investigate the thermodynamic and dynamic properties of stretched and supercooled water. We locate the liquid–gas spinodal, and confirm that the spinodal pressure increases monotonically with T, supporting thermodynamic scenarios for the phase behavior of supercooled water involving a “non-reentrant” spinodal. The dynamics at negative pressure show a minimum in the diffusion constant D when the density is decreased at constant temperature, complementary to the known maximum of D at higher pressures. We locate the loci of minima of D relative to the spinodal, showing that the locus is inside the thermodynamically metastable regions of the phase diagram. These dynamical results reflect the initial enhancement and subsequent breakdown of the tetrahedral structure and of the hydrogen bond network as the density decreases.

Waterlike hierarchy of anomalies in a continuous spherical shouldered potential.

Abstract: We investigate by molecular dynamics simulations a continuous isotropic core-softened potential with attractive well in three dimensions, introduced by Franzese [J. Mol. Liq. 136, 267 (2007)], that displays liquid-liquid coexistence with a critical point and waterlike density anomaly. Besides the thermodynamic anomalies, here we find diffusion and structural anomalies. The anomalies, not observed in the discrete version of this model, occur with the same hierarchy that characterizes water. We discuss the differences in the anomalous behavior of the continuous and the discrete model in the framework of the excess entropy, calculated within the pair correlation approximation.

Structural anomalies for a three dimensional isotropic core-softened potential

Abstract: Using molecular dynamics simulations we investigate the structure of a system of particles interacting through a continuous core-softened interparticle potential. We found for the translational order parameter t a local maximum at a density ρt-max and a local minimum at ρt-min>ρt-max. Between ρt-max and ρt-min, the t parameter anomalously decreases upon increasing pressure. For the orientational order parameter Q6 a maximum was observed at a density ρt-max<ρQmax<ρt-min. For densities between ρQmax and ρt-min, both the translational (t) and orientational (Q6) order parameters have anomalous behavior. We know that this system also exhibits density and diffusion anomalies. We found that the region in the pressure-temperature phase diagram of the structural anomaly englobes the region of the diffusion anomaly that is larger than the region limited by the temperature of maximum density. This cascade of anomalies (structural, dynamic, and thermodynamic) for our model has the same hierarchy as that observed for ...

Static and Dynamic Properties of Stretched Water

Abstract: We present the results of molecular dynamics simulations of the extended simple point charge model of water to investigate the thermodynamic and dynamic properties of stretched and supercooled water. We locate the liquid–gas spinodal, and confirm that the spinodal pressure increases monotonically with T, supporting thermodynamic scenarios for the phase behavior of supercooled water involving a “non-reentrant” spinodal. The dynamics at negative pressure show a minimum in the diffusion constant D when the density is decreased at constant temperature, complementary to the known maximum of D at higher pressures. We locate the loci of minima of D relative to the spinodal, showing that the locus is inside the thermodynamically metastable regions of the phase diagram. These dynamical results reflect the initial enhancement and subsequent breakdown of the tetrahedral structure and of the hydrogen bond network as the density decreases.

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。

Bose-Einstein condensation in a gas of sodium atoms

Abstract: Bose-Einstein condensation (BEC) has been observed in a dilute gas of sodium atoms. A Bose-Einstein condensate consists of a macroscopic population of the ground state of the system, and is a coherent state of matter. In an ideal gas, this phase transition is purely quantum-statistical. The study of BEC in weakly interacting systems which can be controlled and observed with precision holds the promise of revealing new macroscopic quantum phenomena that can be understood from first principles.