Avijit Ghosh

Bio: Avijit Ghosh is an academic researcher from Indian Grassland and Fodder Research Institute. The author has contributed to research in topics: Soil carbon & Soil water. The author has an hindex of 28, co-authored 121 publications receiving 2639 citations. Previous affiliations of Avijit Ghosh include Indian Institute of Technology Bombay & Cornell University.

Generalized Born Model Based on a Surface Integral Formulation

Abstract: We have derived a surface-area-based version of the generalized Born model (S-GB) as a well-defined approximation to the boundary element formulation of the Poisson−Boltzmann (PB) equation. The relationship of the surface area methodology to the volume-integration-based approach of Still and co-workers is elucidated. On the basis of insights obtained from these results, we then develop empirical correction schemes which yield significant improvements in accuracy, as compared to the uncorrected GB model, in reproducing accurate solutions of the Poisson−Boltzmann equation. A large suite of energetic comparisons of GB, corrected S-GB, and PB for multiple conformations of peptides and proteins is presented.

An atomically detailed study of the folding pathways of protein A with the stochastic difference equation.

Abstract: An algorithm is applied here to compute folding pathways of staphylococcal protein A, fragment B. Emphasis is on studies of the complete process, starting from an ensemble of fully denatured conformations and ending at the folded state. The stochastic difference equation algorithm is based on optimization of an action that makes it possible to use a large integration step. Motions with typical displacements that change rapidly on the size scale of the step are filtered out, providing numerically stable and approximate solutions. The present approach is unique in maintaining an atomically detailed picture while providing a systematic, controlled approximation to the classical equations of motion. Analysis of 130 trajectories suggests the following folding mechanism for protein A: At an early precollapse phase of the process, a few native hydrogen bonds form near the C terminus of the protein. The hydrogen bonds are formed mostly within the third helix. The next step is chain collapse that occurs in parallel to additional growth of secondary structure seeds. Therefore, the present study does not support a pure hydrophobic collapse, or substantial early formation of secondary structure. At the last step, native tertiary contacts are formed at the same time as the completion of the secondary structure elements. To a large extent, the process is parallel and not sequential. The early formation of the third helix of protein A, fragment B (in the calculation), is consistent with experimental data.

Long-term fertilization effects on soil organic carbon sequestration in an Inceptisol

Abstract: Limited information is available on long-term fertilization impacts on soil organic carbon (SOC) sequestration in deep soils and C pools within bulk soils and aggregates. Hence, the major objectives of this study were to evaluate long-term (44 years) fertilization impacts on: (i) soil aggregation, labile and recalcitrant C pools within bulk soils and aggregates and (ii) deep soil C accumulation versus sequestration. Treatments were: no mineral fertilizer or manure (control), 100% recommended dose of nitrogen (N), N and phosphorus (NP), N, P and potassium (NPK), 150% recommended NPK (150% NPK), and NPK + farmyard manure (FYM) (NPK + FYM). Labile C, recalcitrant C, total SOC and glomalin in bulk soils and their aggregates were determined in the 0–15 and 15–30 cm soil layers. In addition, total SOC, labile and recalcitrant C contents were measured in the 30–60 and 60–90 cm soil layers. Results revealed that C accumulation and sequestration in NPK + FYM over control plots were 0.74 and 0.22 Mg C ha−1 yr−1, respectively, in 0–90 cm soil layer with >50% of the accumulated C in deep soil layers (30–90 cm). In 0–15 cm layer, despite NPK + FYM and NPK plots had similar amounts of soil macroaggregates, microaggregates were 27% higher with NPK + FYM than NPK, causing higher aggregate stability. Plots with NPK and NPK + FYM had more labile: recalcitrant C ratios in bulk soils than control, NP and N plots. The NPK + FYM plots also had highest recalcitrant C pools within macro- and microaggregates. Glomalin was generally positively correlated with all labile C pools in both soil layers. Additionally, mean weight diameter (MWD) was positively correlated with aggregate-associated C and glomalin within bulk soils. Overall, NPK + FYM management practice not only had higher C accumulation and sequestration in surface and deep soils, but also had better aggregation and ∼26% greater carbon management index than NPK in soil surface and hence should be adopted.

New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model

Abstract: A new linear interaction energy (LIE) method based on a continuum solvent surface generalized Born (SGB) model is proposed for protein−ligand binding affinity calculations. The new method SGB-LIE is about 1 order of magnitude faster than previously published LIE methods based on explicit solvents. It has been applied to several binding sets: HEPT analogues binding to HIV-1 reverse transcriptase (20 ligands), sulfonamide inhibitors binding to human thrombin (seven ligands), and various ligands binding to coagulation factor Xa (eight ligands). The SGB-LIE predictions and cross-validation results show that about 1.0 kcal/mol accuracy is achievable for binding sets with as many as 20 ligands, e.g., for the HIV-1RT binding set, RMS errors of 1.07 and 1.20 kcal/mol are achieved for LIE fitting and leave-one-out cross validation, respectively, with correlation coefficients r2 equal to 0.774 and 0.717. We have also explored various techniques for the LIE underlying conformation space sampling, including molecula...

CHARMM: the biomolecular simulation program.

Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

Climate change 2014 - Mitigation of climate change

Abstract: The talk with present the key results of the IPCC Working Group III 5th assessment report. Concluding four years of intense scientific collaboration by hundreds of authors from around the world, the report responds to the request of the world's governments for a comprehensive, objective and policy neutral assessment of the current scientific knowledge on mitigating climate change. The report has been extensively reviewed by experts and governments to ensure quality and comprehensiveness.

Docking and scoring in virtual screening for drug discovery: methods and applications.

Abstract: Computational approaches that 'dock' small molecules into the structures of macromolecular targets and 'score' their potential complementarity to binding sites are widely used in hit identification and lead optimization Indeed, there are now a number of drugs whose development was heavily influenced by or based on structure-based design and screening strategies, such as HIV protease inhibitors Nevertheless, there remain significant challenges in the application of these approaches, in particular in relation to current scoring schemes Here, we review key concepts and specific features of small-molecule-protein docking methods, highlight selected applications and discuss recent advances that aim to address the acknowledged limitations of established approaches

Exploring protein native states and large-scale conformational changes with a modified generalized born model.

Abstract: Implicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous solvation. Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large-scale conformational transitions, such as protein folding. In contrast to an earlier GB model (implemented in the AMBER-6 program), the improved version does not overstabilize the native structures relative to the finite-difference Poisson–Boltzmann continuum treatment. In addition to improving the energy balance between folded and unfolded conformers, the algorithm (available in the AMBER-7 and NAB molecular modeling packages) is shown to perform well in more than 50 ns of native-state molecular dynamics (MD) simulations of thioredoxin, protein-A, and ubiquitin, as well as in a simulation of Barnase/Barstar complex formation. For thioredoxin, various combinations of input parameters have been explored, such as the underlying gas-phase force fields and the atomic radii. The best performance is achieved with a previously proposed modification to the torsional potential in the Amber ff99 force field, which yields stable native trajectories for all of the tested proteins, with backbone root-mean-square deviations from the native structures being ∼1.5 A after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 A relative to the crystal structure of the complex. Proteins 2004;55:000–000. © 2004 Wiley-Liss, Inc.