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Chacko S.,Thematic Unit of Excellence on Computational Materials Science | Nafday D.,se National Center For Basic Science | Kanhere D.G.,University of Pune | Saha-Dasgupta T.,Thematic Unit of Excellence on Computational Materials Science
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

We investigate the many-body-instability-driven electronic, magnetic, and thermodynamic properties of graphene nanoflakes described by an extended Hubbard model using exact diagonalization. Our exact results lead to a complete magnetic phase diagram in n-V space, where n is the filling and V is the nonlocal Coulomb interaction. The phase diagram is found to consist of reentrant phases with net magnetic moment, separated by those with zero magnetic moment. The interplay of local and nonlocal Coulomb interaction, geometry, and filling gives rise to complex magnetic phases with coexisting antiferromagnetic and ferromagnetic correlations, of both short-range and long-range nature. A small change in temperature or in the strength of the nonlocal Coulomb interaction is found to drive the change in the magnetic state. The low-temperature thermodynamic behavior, driven by the crossover of eigenstates of contrasting magnetic characters, is signaled by a sharp peak in the specific heat. © 2014 American Physical Society. Source

Goyal S.,Banasthali University | Grover S.,Jawaharlal Nehru University | Dhanjal J.K.,Jawaharlal Nehru University | Goyal M.,Banasthali University | And 3 more authors.
Journal of Molecular Modeling | Year: 2014

Leishmaniasis is an endemic disease caused by infection with one of several different species of protozoan parasite Leishmania. Oligopeptidase B (OPB) is a serine peptidase which plays a vital role in survival of the Leishmania parasite in the host (human) macrophage and help in attaining complete virulence. Inhibition of this peptidase would check the parasite growth inside the host organism and would thus control its infection. Lack of efficient and cheap drugs has led to an urgent need for development of new anti-leishmanial drugs and this study is a step forward in this direction. Using a structure-based approach we virtually screened a large naturally-occurring compound library against OPB and subjected two top scoring compounds with high binding affinity to molecular dynamics simulations which showed a stable RMSD trajectory. The first compound COP (Glide score: -13.183) was found stable for 15 ns at RMSD of 2.5 Å while the second compound TOA (Glide score: -10.308) was stable for 8 ns at RMSD of 1.5 Å. The screened compounds interacted with some crucial residues of OPB such as COP interacted with Ser577 and His697 (part of the catalytic triad), Tyr499 (responsible for substrate stability), Arg576 (conserved in protozoan family) and Arg664 (plays a role in stabilization of the bound inhibitor). TOA also interacted with Glu669 (conserved in protozoan family) in addition to the residues interacted with COA. These interactions are crucial for OPB inhibition. This study identified naturally-occurring compound leads against OPB with good binding affinity and low toxicity to human cells. © 2014 Springer-Verlag. Source

Moitra A.,Thematic Unit of Excellence on Computational Materials Science
Computational Materials Science | Year: 2013

The strength of nanocrystalline (NC) hexagonal closed packed (hcp) magnesium has been studied using computer simulations. Three dimensional NC magnesium materials are developed using Voronoi tessellation in which a random distribution of grains is generated. The microstructural properties and mechanical behaviors under tensile loading are investigated using molecular dynamics simulations. A size scale effect related to the yield stress in the specimen is evidenced. A transition from grain size softening to grain size hardening has been observed for a 10 nm average grain size. © 2013 Elsevier B.V. All rights reserved. Source

Sikdar S.,Sn Bose National Center For Basic Science | Chakrabarti J.,Sn Bose National Center For Basic Science | Chakrabarti J.,Thematic Unit of Excellence on Computational Materials Science | Ghosh M.,Sn Bose National Center For Basic Science
Molecular BioSystems | Year: 2014

We show that the thermodynamics of metal ion-induced conformational changes aid to understand the functions of protein complexes. This is illustrated in the case of a metalloprotein, alpha-lactalbumin (aLA), a divalent metal ion binding protein. We use the histograms of dihedral angles of the protein, generated from all-atom molecular dynamics simulations, to calculate conformational thermodynamics. The thermodynamically destabilized and disordered residues in different conformational states of a protein are proposed to serve as binding sites for ligands. This is tested for β-1,4-galactosyltransferase (β4GalT) binding to the Ca2+-aLA complex, in which the binding residues are known. Among the binding residues, the C-terminal residues like aspartate (D) 116, glutamine (Q) 117, tryptophan (W) 118 and leucine (L) 119 are destabilized and disordered and can dock β4GalT onto Ca2+-aLA. No such thermodynamically favourable binding residues can be identified in the case of the Mg2+-aLA complex. We apply similar analysis to oleic acid binding and predict that the Ca2+-aLA complex can bind to oleic acid through the basic histidine (H) 32 of the A2 helix and the hydrophobic residues, namely, isoleucine (I) 59, W60 and I95, of the interfacial cleft. However, the number of destabilized and disordered residues in Mg2+-aLA are few, and hence, the oleic acid binding to Mg2+-bound aLA is less stable than that to the Ca2+-aLA complex. Our analysis can be generalized to understand the functionality of other ligand bound proteins. © the Partner Organisations 2014. Source

Das A.,Sn Bose National Center For Basic Science | Chakrabarti J.,Sn Bose National Center For Basic Science | Chakrabarti J.,Thematic Unit of Excellence on Computational Materials Science | Ghosh M.,Sn Bose National Center For Basic Science
Chemical Physics Letters | Year: 2013

Conformational changes in proteins induced by metal-ions play extremely important role in various cellular processes and technological applications. Dihedral angles are suitable conformational variables to describe microscopic conformations of a biomacromolecule. Here, we use the histograms of the dihedral angles to study the thermodynamics of conformational changes of a protein upon metal-ion binding. Our method applied to Ca2+ ion binding to an important metalloprotein, Calmodulin, reveals different thermodynamic changes in different metal-binding sites. The ligands coordinating to Ca2+ ions also play different roles in stabilizing the metal-ion coordinated protein-structure. Metal-ion binding induce remarkable thermodynamic changes in distant part of the protein via modification of secondary structural elements. © 2013 Elsevier B.V. All rights reserved. Source

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