Charusita Chakravarty

Bio: Charusita Chakravarty is an academic researcher from Indian Institute of Technology Delhi. The author has contributed to research in topics: Path integral Monte Carlo & Monte Carlo method. The author has an hindex of 37, co-authored 122 publications receiving 3901 citations. Previous affiliations of Charusita Chakravarty include University of Cambridge & Indian Institutes of Technology.

Water: A Tale of Two Liquids

Abstract: Water is the most abundant liquid on earth and also the substance with the largest number of anomalies in its properties. It is a prerequisite for life and as such a most important subject of current research in chemical physics and physical chemistry. In spite of its simplicity as a liquid, it has an enormously rich phase diagram where different types of ices, amorphous phases, and anomalies disclose a path that points to unique thermodynamics of its supercooled liquid state that still hides many unraveled secrets. In this review we describe the behavior of water in the regime from ambient conditions to the deeply supercooled region. The review describes simulations and experiments on this anomalous liquid. Several scenarios have been proposed to explain the anomalous properties that become strongly enhanced in the supercooled region. Among those, the second critical-point scenario has been investigated extensively, and at present most experimental evidence point to this scenario. Starting from very low ...

Entropy, diffusivity, and structural order in liquids with waterlike anomalies.

Abstract: The excess entropy, defined as the difference between the entropies of the liquid and the ideal gas under identical density and temperature conditions, is studied as a function of density and temperature for liquid silica and a two-scale ramp potential, both of which are known to possess waterlike liquid state anomalies. The excess entropy for both systems is evaluated using a fairly accurate pair correlation approximation. The connection between the excess entropy and the density and diffusional anomalies is demonstrated. Using the pair correlation approximation to the excess entropy, it can be shown that if the energetically favorable local geometries in the low and high density limits have different symmetries, then a structurally anomalous regime can be defined in terms of orientational and translational order parameters, as in the case of silica and the two-scale ramp system but not for the one-scale ramp liquid. Within the category of liquids with waterlike anomalies, we show that the relationship between the macroscopic entropy and internal energy is sufficient to distinguish between those with local anisotropy and consequent open packings at low densities and those with isotropic interactions but multiple length scales. Since it is straightforward to evaluate the pair correlation entropy and internal energy from simulations or experimental data, such plots should provide a convenient means to diagnose the existence as well as type of anomalous behavior in a range of liquids, including ionic and intermetallic melts and complex fluids with ultrasoft repulsions.

Excess entropy, Diffusivity and Structural Order in liquids with water-like anomalies

Abstract: The excess entropy, Se, defined as the difference between the entropies of the liquid and the ideal gas under identical density and temperature conditions, is shown to be the critical quantity connecting the structural, diffusional and density anomalies in water-like liquids. Based on simulations of silica and the two-scale ramp liquids, water-like density and diffusional anomalies can be seen as consequences of a characteristic non-monotonic density dependence of Se. The relationship between excess entropy, the order metrics and the structural anomaly can be understood using a pair correlation approximation to Se.

Excess entropy scaling of transport properties of Lennard-Jones chains

Abstract: Excess-entropy scaling relationships for diffusivity and viscosity of Lennard-Jones chain fluids are tested using molecular dynamics simulations for chain sizes that are sufficiently small that chain entanglement effects are insignificant. The thermodynamic excess entropy Se is estimated using self-associating fluid theory (SAFT). A structural measure of the entropy S2 is also computed from the monomer-monomer pair correlation function, gm(r). The thermodynamic and structural estimators for the excess entropy are shown to be very strongly correlated. The dimensionless center-of-mass diffusivities, Dcm*, obtained by dividing the diffusivities by suitable macroscopic reduction parameters, are shown to conform to the excess entropy scaling relationship, Dcm*=Anexp(αnSe), where the scaling parameters depend on the chain length n. The exponential parameter αn varies as −(1∕n) while An varies approximately as n−0.5. The scaled viscosities obey a similar relationship with scaling parameters Bn and βn where βn va...

Thermodynamic, diffusional, and structural anomalies in rigid-body water models.

Abstract: Structural, density, entropy, and diffusivity anomalies of the TIP4P/2005 model of water are mapped out over a wide range of densities and temperatures. The locus of temperatures of maximum density (TMD) for this model is very close to the experimental TMD locus for temperatures between 250 and 275 K. Four different water models (mTIP3P, TIP4P, TIP5P, and SPC/E) are compared with the TIP4P/2005 model in terms of their anomalous behavior. For all the water models, the density regimes for anomalous behavior are bounded by a low-density limit at around 0.85-0.90 g cm(-3) and a high-density limit at about 1.10-1.15 g cm(-3). The onset temperatures of the density anomaly in the various models show a much greater variation, ranging from 202 K for mTIP3P to 289 K for TIP5P. The order maps for the various water models are qualitatively very similar with the structurally anomalous regions almost superimposable in the q(tet)-τ plane. Comparison of the phase diagrams of water models with the region of liquid-state anomalies shows that the crystalline phases are much more sensitive to the choice of water models than the liquid state anomalies; for example, SPC/E and TIP4P/2005 show qualitatively similar liquid state anomalies but very different phase diagrams. The anomalies in the liquid in all the models occur at much lower pressures than those at which the melting line changes from negative to positive slope. The results in this study demonstrate several aspects of structure-entropy-diffusivity relationships of water models that can be compared with experiment and used to develop better atomistic and coarse-grained models for water.

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。

PACKMOL: a package for building initial configurations for molecular dynamics simulations.

Abstract: Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/.

Path integrals in the theory of condensed helium

Abstract: One of Feynman's early applications of path integrals was to superfluid $^{4}\mathrm{He}$. He showed that the thermodynamic properties of Bose systems are exactly equivalent to those of a peculiar type of interacting classical "ring polymer." Using this mapping, one can generalize Monte Carlo simulation techniques commonly used for classical systems to simulate boson systems. In this review, the author introduces this picture of a boson superfluid and shows how superfluidity and Bose condensation manifest themselves. He shows the excellent agreement between simulations and experimental measurements on liquid and solid helium for such quantities as pair correlations, the superfluid density, the energy, and the momentum distribution. Major aspects of computational techniques developed for a boson superfluid are discussed: the construction of more accurate approximate density matrices to reduce the number of points on the path integral, sampling techniques to move through the space of exchanges and paths quickly, and the construction of estimators for various properties such as the energy, the momentum distribution, the superfluid density, and the exchange frequency in a quantum crystal. Finally the path-integral Monte Carlo method is compared to other quantum Monte Carlo methods.

On representing chemical environments

Abstract: We review some recently published methods to represent atomic neighborhood environments, and analyze their relative merits in terms of their faithfulness and suitability for fitting potential energy surfaces. The crucial properties that such representations (sometimes called descriptors) must have are differentiability with respect to moving the atoms and invariance to the basic symmetries of physics: rotation, reflection, translation, and permutation of atoms of the same species. We demonstrate that certain widely used descriptors that initially look quite different are specific cases of a general approach, in which a finite set of basis functions with increasing angular wave numbers are used to expand the atomic neighborhood density function. Using the example system of small clusters, we quantitatively show that this expansion needs to be carried to higher and higher wave numbers as the number of neighbors increases in order to obtain a faithful representation, and that variants of the descriptors converge at very different rates. We also propose an altogether different approach, called Smooth Overlap of Atomic Positions, that sidesteps these difficulties by directly defining the similarity between any two neighborhood environments, and show that it is still closely connected to the invariant descriptors. We test the performance of the various representations by fitting models to the potential energy surface of small silicon clusters and the bulk crystal.