Prabal K. Maiti

Bio: Prabal K. Maiti is an academic researcher from Indian Institute of Science. The author has contributed to research in topics: Dendrimer & Molecular dynamics. The author has an hindex of 45, co-authored 222 publications receiving 6842 citations. Previous affiliations of Prabal K. Maiti include National Centre for Biological Sciences & Saha Institute of Nuclear Physics.

Binding of DNA nucleobases and nucleosides with graphene.

Abstract: Interaction of two different samples of graphene with DNA nucleobases and nucleosides is investigated by isothermal titration calorimetry. The relative interaction energies of the nucleobases decrease in the order guanine (G) > adenine (A) > cytosine (C) > thy mine (T) in aqueous solutions, although the positions of C and T seem to be interchangeable. The same trend is found with the nucleosides. Interaction energies of the A-T and G-C pairs are somewhere between those of the constituent bases. Theoretical calculations including van der Wools interaction and solvation energies give the trend G > A similar to T > C. The magnitudes of the interaction energies of the nucleobases with graphene are similar to those found with single-walled carbon nonotubes.

Structure of PAMAM dendrimers: Generations 1 through 11

Abstract: The structure and dynamics of poly(amido amide) (PAMAM) dendrimers have been of great interest both scientifically and industrially, but such important features as the distributions of atoms, channels, and strain inside these molecules remain unresolved. This paper reports results from systematic investigations of the atomistic structure of ethylenediamine (EDA) cored PAMAM dendrimer up through the 11th generation (294 852 atoms), at which point the strain energy has risen to a point that limits uniform growth of additional layers. Here we report, as a function of generation, structural properties such as radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, solvent accessible surface area, molecular volume, and end group distribution functions, all evaluated from extensive molecular dynamics (MD) at 300 K. We find that the radius of gyration scales as Rg ∼ N1/3 over the entire range of generations, suggesting rather uniform space filling for all generations. Contrary to common expectation, we find that the outer subgenerations penetrate substantially into the interior of the dendrimer, even for G11. Consequently, the terminal amine groups are distributed throughout the interior, not just on the periphery of the dendrimer. However for G6 through G11 there is a large region of uniform density, supporting the uniform scattering model often used in interpreting the SANS (small-angle neutron scattering) and SAXS (small-angle X-ray scattering) data, which lead to sizes in excellent agreement with the calculations. The calculated single particle form factor approaches that of a sphere as the generation number increases. For the larger generations, we found that the use of continuous configuration biased Monte Carlo (CCBB MC) was essential to construct initial configurations that lead to lower final strain energies.

Effect of Solvent and pH on the Structure of PAMAM Dendrimers

Abstract: We report various structural and conformational properties of generations 4, 5, and 6 PAMAM (polyamidoamine) dendrimer [EDA (ethylenediamine) core)] at various protonation levels through extensive molecular dynamics (MD) simulations in explicit solvent. The presence of solvent leads to swelling of the dendrimer (by 33% for G5 compared to the case of no solvent). We find that decreasing the solution from high pH (∼10, no protonation) to neutral (∼7, only primary amines protonated) to low pH (∼4, tertiary amines also protonated) changes the radius of gyration of G5 from 21 to 22 to 25 A, respectively. We also report such other structural quantities as radial density, distribution of terminal groups, solvent accessible surface area and volume, shape, and structure factors (to compare with SAXS and SANS experiments) at various pH conditions. We find significant back-folding of the outer subgenerations in the interior of the molecules at all levels of pH, contrary to original expectations and some SANS experiments but in agreement with other SANS experiments. We find significant water penetration inside the dendrimer, with ∼3 water/tertiary amine for high pH and ∼6 water/tertiary amine for low pH (all for G5). This indicates that the interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules, suggesting using PAMAM dendrimer for guest−host applications. This estimate of internal waters suggests that sufficient water is available to facilitate metal ion binding.

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Abstract: Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Molecular Dynamics Study of a Surfactant-Mediated Decane-Water Interface: Effect of Molecular Architecture of Alkyl Benzene Sulfonate

Abstract: The effect of molecular architecture of a surfactant, particularly the attachment position of benzene sulfonate on the hexadecane backbone, at the decane−water interface was investigated using atomistic MD simulations. We consider a series of surfactant isomers in the family of alkyl benzene sulfonates, denoted by m-C16, indicating a benzene sulfonate group attached to the mth carbon in a hexadecane backbone. The equilibrated model systems showed a well-defined interface between the decane and water phases. We find that surfactant 4-C16 has a more compact packing, in terms of the interfacial area and molecular alignment at the interface, than other surfactants simulated in this study. Furthermore, surfactant 4-C16 leads to the most stable interface by having the lowest interface formation energy. The interfacial thickness is the largest in the case of surfactant 4-C16, with the thickness decreasing when the benzene sulfonate is located farther from the attachment position of 4-C16 (the 4th carbon). The interfacial tension profile was calculated along the direction perpendicular to the interface using the Kirkwood−Buff theory. From the comparison of the interfacial tension obtained from the interfacial tension profile, we found that surfactant 4-C16 induces the lowest interfacial tension and that the interfacial tension increases with decreasing interfacial thickness as a function of the attachment position of benzene sulfonate. Such a relationship between the interfacial thickness and interfacial tension is rationalized in terms of the miscibility of the alkyl tail of surfactant m-C16 with decane by comparing the “effective” length of the alkyl tail with the average end-to-end length of decane. Among the surfactants, the effective length of the 4-C16 alkyl tail (9.53 ± 1.36 A) was found to be closest to that of decane (9.97 ± 1.03 A), which is consistent with the results from the density profile and the interfacial tension profile.

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。

Graphene: The New Two-Dimensional Nanomaterial

Abstract: Every few years, a new material with unique properties emerges and fascinates the scientific community, typical recent examples being high-temperature superconductors and carbon nanotubes. Graphene is the latest sensation with unusual properties, such as half-integer quantum Hall effect and ballistic electron transport. This two-dimensional material which is the parent of all graphitic carbon forms is strictly expected to comprise a single layer, but there is considerable interest in investigating two-layer and few-layer graphenes as well. Synthesis and characterization of graphenes pose challenges, but there has been considerable progress in the last year or so. Herein, we present the status of graphene research which includes aspects related to synthesis, characterization, structure, and properties.

Methods in Enzymology.

Abstract: I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …