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@inproceedings{bib_Quan_2022, AUTHOR = {Sahoo, Shweta and UTKARSH, and Singh, Harjinder }, TITLE = {Quantum phase recognition using quantum tensor networks}, BOOKTITLE = {The European Physical Journal Plus}. YEAR = {2022}}

Machine learning (ML) has recently facilitated many advances in solving problems related to many-body physical systems. Given the intrinsic quantum nature of these problems, it is natural to speculate that quantum-enhanced machine learning will enable us to unveil even greater details than we currently have. With this motivation, this paper examines a quantum machine learning approach based on shallow variational ansatz inspired by tensor networks for supervised learning tasks. In particular, we first look at the standard image classification tasks using the FashionMNIST dataset and study the effect of repeating tensor network layers on ansatz’s expressibility and performance. Finally, we use this strategy to tackle the problem of quantum phase recognition for the transverse-field Ising and Heisenberg spin models in one and two dimensions, where we were able to reach ≥ 98% test-set accuracies with both multi-scale entanglement renormalization ansatz (MERA) and tree tensor network (TTN) inspired parametrized quantum circuits. Keywords: Quantum Computing, Quantum Machine Learning, Quantum Many-body Systems, QuantumClassical Algorithms

@inproceedings{bib_Qubi_2022, AUTHOR = {Sinha, Animesh and UTKARSH, and Singh, Harjinder }, TITLE = {Qubit Routing Using Graph Neural Network Aided Monte Carlo Tree Search}, BOOKTITLE = {AAAI Conference on Artificial Intelligence}. YEAR = {2022}}

Near-term quantum hardware can support two-qubit operations only on the qubits that can interact with each other. Therefore, to execute an arbitrary quantum circuit on the hardware, compilers have to frst perform the task of qubit routing, i.e., to transform the quantum circuit either by inserting additional SWAP gates or by reversing existing CNOT gates to satisfy the connectivity constraints of the target topology. The depth of the transformed quantum circuits is minimized by utilizing the Monte Carlo tree search (MCTS) to perform qubit routing by making it both construct each action and search over the space of all actions. It is aided in performing these tasks by a Graph neural network that evaluates the value function and action probabilities for each state. Along with this, we propose a new method of adding mutex-lock like variables in our state representation which helps factor in the parallelization of the scheduled operations, thereby pruning the depth of the output circuit. Overall, our procedure (referred to as QRoute) performs qubit routing in a hardware agnostic manner, and it outperforms other available qubit routing implementations on various circuit benchmarks.

@inproceedings{bib_Quan_2022, AUTHOR = {UTKARSH, and Singh, Harjinder }, TITLE = {Quantum Chemistry Calculations using Energy Derivatives on Quantum Computers}, BOOKTITLE = {Chemical Physics}. YEAR = {2022}}

Quantum chemistry calculations such as the prediction of molecular properties and modeling of chemical reactions are a few of the critical areas where near-term quantum computers can showcase quantum advantage. We present a method to calculate energy derivatives for both ground state and excited state energies with respect to the parameters of a chemical system based on the framework of the variational quantum eigensolver (VQE). A low-depth implementation of quantum circuits within the hybrid variational paradigm is designed, and their computational costs are analyzed. We showcase the effectiveness of our method by incorporating it in some key quantum chemistry applications of energy derivatives, such as to perform minimum energy configuration search and estimate molecular response properties estimation of H2 molecule, and also to find the transition state of H2 + H ↔ H + H2 reaction. The obtained results are shown to be in complete agreement with their respective full configuration interaction (FCI) values. Keywords: Quantum Computing, Quantum Chemistry, Variational Quantum Eigensolver, Hybrid QuantumClassical Algorithms

@inproceedings{bib_A_mi_2021, AUTHOR = {ALVA, ADRIAN JOSEPH and Singh, Harjinder }, TITLE = {A minimal model for synaptic integration in simple neurons}, BOOKTITLE = {Physica D}. YEAR = {2021}}

Synaptic integration is a prominent aspect of neuronal information processing. The detailed mechanisms that modulate synaptic inputs determine the computational properties of any given neuron. We study a simple model for the summation of excitatory inputs from synapses and illustrate its use by characterizing some functional properties of postsynaptic neurons. In this regard, we study the response of postsynaptic neurons as defined by the model to two well known noise driven processes: stochastic and coherence resonance. The model requires a small number of parameters and is especially useful to isolate the role of integration mechanisms that rely on summation of inputs with little dendritic processing.

@inproceedings{bib_An_A_2020, AUTHOR = {V, Suresh Kumar N and Singh, Harjinder }, TITLE = {An APT charge based descriptor for atomic level description of chemical Raman enhancement by adsorption of 4-Mercaptopyridine on semiconducting nanaoclusters: A theoretical study}, BOOKTITLE = {Vibrational Spectroscopy}. YEAR = {2020}}

Density functional theory (DFT) based calculations are carried out to study effect of molecular charge on both the binding energy as well as chemical Raman enhancement of deprotonated 4-Mercaptopyridine (ligand) bound to the semiconducting nanocluster, Zn3Se3 and metal substituted nanoclusters, Zn2MSe3 (M: Ag, Cu). Change of molecular charge from 0 to −1 increases binding energy of the ligand for Zn3Se3 cluster and decreases Raman activity of vibrational modes. On the other hand, the ligand bound to the metal substituted nanoclusters, Zn2MSe3 shows minimal decrease in binding energy and a noteworthy enhancement in Raman activity of the vibrational modes, on varying the molecular charge from 0 to −1. Static Raman activities of vibrational modes are analyzed using change of molecular polarizability components with normal coordinates of the modes. An APT (Atomic Polar Tensor) charge based descriptor is used for characterization of the chemical Raman enhancement. The descriptor measures substrate induced charge concentration per unit displacement of an atom involved in a mode of vibration. We also show that significantly enhanced intensity of vibrational modes is associated with atoms of relatively greater magnitudes of the APT charge based descriptor

@inproceedings{bib_Cont_2019, AUTHOR = {Nandipati, K. R. and Kanakati, Arun Kumar and Singh, Harjinder and Mahapatra, Susanta }, TITLE = {Controlled intramolecular H-transfer in Malonaldehyde in the electronic ground state mediated through the conical intersection of 1n and 1 excited electronic states}, BOOKTITLE = {Physical Chemistry Chemical Physics}. YEAR = {2019}}

We report photo-isomerization of malonaldehyde in its electronic ground state (S0), mediated by coupled 1nπ∗ (S1) - 1ππ∗ 10 (S2) electronic excited states, accomplished with the aid of optimally 11 designed ultraviolet (UV)-laser pulses. In particular, the control of H-transfer from a configuration 12 predominantly located in the left well (say, reactant) to that in the right well (say, product) of the 13 electronic ground S0 potential energy surface is achieved by a pump-dump mechanism including 14 the nonadiabatic interactions between the excited S1 and S2 states. An interplay between the 15 nonadiabatic coupling due to conical intersection of the S1 and S2 states and the laser-molecule 16 interaction is found to be imprinted in the time-dependent electronic population. The latter is also 17 examined by employing optimal fields of varying intensity and frequency of the UV laser pulses. 18 For the purpose of the present study, we constructed a three-states and two-modes coupled diabatic 19 Hamiltonian with the help of adiabatic electronic energies and transition dipole moments calculated 20 by ab initio quantum chemistry methods. The electronic diabatic model is developed using the 21 calculated adiabatic energies of the two excited electronic states (S1 and S2) in order to carry out the 22 dynamics study. The optimal fields for achieving the controlled isomerization are designed within 23 the framework of optimal control theory employing the optimization technique of a multitarget 24 functional using the genetic algorithm. The laser-driven dynamics of the system is treated by 25 numerically solving the time-dependent Schr¨odinger equation within the dipole approximation. 26 Time-averaged yield of the target prod

@inproceedings{bib_Cont_2017, AUTHOR = {Singh, Harjinder }, TITLE = {Controlling Nuclear and Electronic Motion in Molecules}, BOOKTITLE = {Excellence in Science}. YEAR = {2017}}

We will present our work on controlling nuclear and electronic motion in molecules using laser pulses designed using Optimal control theory (OCT). The control problem is formulated as the maximization of cost functional made of an objective function along with the constraints on the field fluence. The objective function has the prescribed dynamical goals. A detailed analysis of the optimal pulse reveals complex path-ways to arrive at seemingly simple goals. We have used OCT to obtain infrared laser pulses for the selective vibrational excitation of several different systems, from a simple diatomic to triatomic systems located in complex molecular environments. Controlled initiation of intramolecular H-transfer in malonaldehyde using ultrashort uv-laser pulses through an optically bright electronic excited state as a mediator will be discussed. Finally, our attempts to control the quantum dynamics of N-H photodissociation of pyrrole via a counterintuitive coupling of electronic states using uv-laser pulses will be discussed.

@inproceedings{bib_An_a_2017, AUTHOR = {Reddy, Nandipati Krishna and Lan, Z. and Singh, Harjinder and Mahapatra, S. }, TITLE = {An alternative laser driven photodissociation mechanism of pyrrole via 1 πσ /S 0 conical intersection}, BOOKTITLE = {The Journal of Chemical Physics}. YEAR = {2017}}

A first principles quantum dynamics study of N–H photodissociation of pyrrole on the coupled electronic states is carried out with the aid of an optimally designed UV-laser pulse. A new photodissociation path, as compared to the conventional barrier crossing on the state, opens up upon electronic transitions under the influence of pump-dump laser pulses, which efficiently populate both the dissociation channels. The interplay of electronic transitions due both to vibronic coupling and the laser pulse is observed in the control mechanism and discussed in detail. The proposed control mechanism seems to be robust, and not discussed in the literature so far, and is expected to trigger future experiments on the photochemistry of molecules of chemical and biological importance. The design of the optimal pulses and their application to enhance the overall dissociation probability is carried out within the framework of optimal control theory. The quantum dynamics of the system in the presence of pulse is treated by solving the time-dependent Schr ̈ odinger equation in the semi-classical dipole approximation

@inproceedings{bib_Init_2017, AUTHOR = {Nandipati, K.R. and Kanakati, Arun Kumar and Singh, Harjinder and Lan, Z. and Mahapatra, S. }, TITLE = {Initial state-specific photodissociation dynamics of pyrrole via 1πσ∗/S0 conical intersection initiated with optimally controlled UV-laser pulses}, BOOKTITLE = {European Physical Journal D}. YEAR = {2017}}

Optimal initiation of quantum dynamics of N-H photodissociation of pyrrole on the S0- 1πσ∗( 1A2) coupled electronic states by UV-laser pulses in an effort to guide the subsequent dynamics to dissociation limits is studied theoretically. Specifically, the task of designing optimal laser pulses that act on initial vibrational states of the system for an effective UV-photodissociation is considered by employing optimal control theory. The associated control mechanism(s) for the initial state dependent photodissociation dynamics of pyrrole in the presence of control pulses is examined and discussed in detail. The initial conditions determine implicitly the variation in the dissociation probabilities for the two channels, upon interaction with the field. The optimal pulse corresponds to the objective fixed as maximization of overall reactive flux subject to constraints of reasonable fluence and quantum dynamics. The simple optimal pulses obtained by the use of genetic algorithm based optimization are worth an experimental implementation given the experimental relevance of πσ∗-photochemistry in recent times.

@inproceedings{bib_Bind_2015, AUTHOR = {RAI, SANDHYA and Singh, Harjinder and U, Deva Priyakumar }, TITLE = {Binding to Gold Nanocluster Alters the Hydrogen Bonding Interactions and Electronic Properties of Canonical and Size Expanded DNA Base Pairs}, BOOKTITLE = {RSC Advances}. YEAR = {2015}}

DNA molecules tagged to metal nanoparticles, especially gold nanoparticles (AuNPs), have been shown to exhibit potential applications in designing and fabrication of novel electronic nano-devices, but the binding mechanism between gold nanoparticles and DNA bases and its implications are not completely understood. In this work, a comprehensive study to examine the effect of structural perturbations offered to DNA base pairs in terms of size expansion and adsorption on a gold cluster (Au3) has been done using density functional theory. Geometric and electronic features of these complexes provide evidences for distortion of certain base pairs depending on the binding site of the cluster. This is further substantiated via normal mode, natural bond orbital (NBO) and atoms in molecules (AIM) analyses. The natural population analysis (NPA) and NBO analysis indicate that complexation greatly affects the charge distribution on the base pairs due to charge transfer between base pair and gold cluster. This charge redistribution may offer a possibility of higher order interactions. Upon complexation, a marked decrease in the HOMO-LUMO gap is observed, which is more profound in cases where size expanded bases are involved due to the extended π-conjugation of the fused benzine rings. This study demonstrates the possibility of combining structural modifications to DNA base pairs and subsequent binding to gold nano particles to modulate and achieve molecular systems with desired optico-electronic properties.

@inproceedings{bib_Theo_2015, AUTHOR = {BHARDWAJ, SHWETA and RAI, SANDHYA and Sau, Tapan Kumar and Singh, Harjinder }, TITLE = {Theoretical studies of Raman scattering properties of methylphosphine and methylamine adsorbed on gold clusters}, BOOKTITLE = {Vibrational Spectroscopy}. YEAR = {2015}}

Recent reports have demonstrated that nanoclusters of silver and gold can act as substrates for Raman signal enhancements. This article presents a density functional theory (DFT)-based study to explore how the variations in the nature of the cluster-binding heteroatom in the ligand molecule and the relative orientation of the alkyl group attached to the heteroatom affect the Raman signal enhancement in the ligand molecules. Our calculations involved nitrogen and phosphorus heteroatoms in two simple model molecules, methylphosphine and methylamine, as ligands and four small gold clusters, Aun (n = 6–9). In order to understand the interactions in the cluster-molecule systems, we have calculated various geometrical parameters such as Au–X (X = P, N) distances, ffC–X–Au angles and different bond lengths of free and cluster-bound molecules as well as various interaction energies. We have performed natural bond order (NBO) analysis and have calculated second order stabilization energies for the molecules bound to the gold clusters from the NBO analysis. In addition, we have performed detailed calculations pertaining to the change in polarisability, quantity of molecule to cluster charge transfer as well as molecular orientations relative to the clusters and have studied how these factors influence the Raman scattering cross-sections and vibrational frequency shifts. The quantity of charge transfer and the orientation effect have been found to be important contributors in the chemical Raman enhancement mechanism of the ligand molecules.

@inproceedings{bib_Bind_2015, AUTHOR = {RAI, SANDHYA and Singh, Harjinder and U, Deva Priyakumar }, TITLE = {Binding to gold nanoclusters alters the hydrogen bonding interactions and electronic properties of canonical and size-expanded DNA base pairs}, BOOKTITLE = {RSC Advances}. YEAR = {2015}}

DNA molecules tagged to metal nanoparticles, especially gold nanoparticles (AuNPs), have been shown to have potential applications in the design and fabrication of novel electronic nano-devices, but the binding mechanism between gold nanoparticles and DNA bases and its implications are not completely understood. In this work, a comprehensive study to examine the effect of structural perturbations caused to DNA base pairs in terms of size expansion and adsorption on a gold cluster (Au3) has been carried out using density functional theory. The geometric and electronic features of these complexes provide evidence for the distortion of certain base pairs depending on the binding site of the cluster. This is further substantiated via normal mode, natural bond orbital (NBO) and atoms in molecules (AIM) analyses. The natural population analysis (NPA) and NBO analysis indicate that complexation greatly affects …

@inproceedings{bib_Opti_2014, AUTHOR = {Nandipati, K.R. and Singh, Harjinder and Reddy, S. Nagaprasad and Kumar, K.A. and Mahapatra, S. }, TITLE = {Optimal initiation of electronic excited state mediated intramolecular H-transfer in malonaldehyde by UV-laser pulses}, BOOKTITLE = {European Physical Journal D}. YEAR = {2014}}

Optimally controlled initiation of intramolecular H-transfer in malonaldehyde is accomplished by designing a sequence of ultrashort (∼80 fs) down-chirped pump-dump ultra violet (UV)-laser pulses through an optically bright electronic excited [S2 (ππ∗)] state as a mediator. The sequence of such laser pulses is theoretically synthesized within the framework of optimal control theory (OCT) and employing the well-known pump-dump scheme of Tannor and Rice [D.J. Tannor, S.A. Rice, J. Chem. Phys. 83, 5013 (1985)]. In the OCT, the control task is framed as the maximization of cost functional defined in terms of an objective function along with the constraints on the field intensity and system dynamics. The latter is monitored by solving the time-dependent Schr¨odinger equation. The initial guess, laser driven dynamics and the optimized pulse structure (i.e., the spectral content and temporal profile) followed by associated mechanism involved in fulfilling the control task are examined in detail and discussed. A comparative account of the dynamical outcomes within the Condon approximation for the transition dipole moment versus its more realistic value calculated ab initio is also presented.

@inproceedings{bib_Dens_2014, AUTHOR = {V, Suresh Kumar N and Singh, Harjinder }, TITLE = {Density Functional Theory Based Study on Cis−Trans Isomerism of the Amide Bond in Homodimers of β2,3- and β3‑Substituted Homoproline}, BOOKTITLE = {Journal of Physical Chemistry A}. YEAR = {2014}}

: Preference for a cis/trans peptide bond between residues of dipeptides formed by substituted β2,3 (I) and β3 (II) homoproline is investigated using density functional theory (DFT). Potential energy surfaces for monomer and linear dimers are explored at the B3LYP/6-31G(d,p) level of theory. Minimum energy conformations of the dipeptides are optimized using B3LYP, PBE1PBE, B97D, and M06-2X functionals at the 6-31G(d,p) level of basis set in both the gas phase and solvent phase. The relative free energy difference between the selected conformations is marginal. Results obtained using the functionals M06-2X and B97D on dimers of I and II, respectively, agree with experimental results. The lowest energy conformations predicted by B97D/6-31G(d,p) and M06-2X/6-31G(d,p) levels of theory show greater relative MP2 correlation energy. Dipeptides of I with hydrophilic substituents show preference for a trans peptide bond. Support for cis/trans isomerism in dimers of I with hydrophobic substituents comes from potential energy surfaces and free energy data. Although dipeptides of II with hydrophilic substituents show preference for cis peptide bond, the dipeptides with hydrophobic substituent prefer trans bond.

@inproceedings{bib_Modu_2014, AUTHOR = {RAI, SANDHYA and RANJAN, SUPRIYA and Singh, Harjinder and U, Deva Priyakumar }, TITLE = {Modulation of structural, energetic and electronic properties of DNA and size-expanded DNA bases upon binding to gold clusters}, BOOKTITLE = {RSC Advances}. YEAR = {2014}}

Gold cluster–nucleobase complexes have potential applications in designing and fabrication of novel electronic nano-devices, and there has been a surge in research activities in this area recently. Binding of gold clusters (Au3 and Au4) with DNA bases and size-expanded DNA bases (x-bases) have been studied using density functional theory employing high quality basis set. A comprehensive attempt has been made to examine several gold–nucleobase complexes with respect to change in the orientation of Au clusters with respect to all the titratable sites of the bases. Geometric and electronic features of these complexes provided evidences for existence of non-conventional hydrogen bonds, which was further substantiated via vibrational frequency and natural bond orbital (NBO) analysis. The nucleobases, both canonical and size-expanded forms, form stable complexes with both the gold clusters considered …

@inproceedings{bib_Corr_2013, AUTHOR = {CHATTERJEE, SOURAV and S.K.Sazim, and Chakrabarty, Indranil and Singh, Harjinder }, TITLE = {Correlating Capability of Non Local Hamiltonian}, BOOKTITLE = {INTERNATIONAL CONFERENCE ON QUANTUM INFORMATION AND QUANTUM COMPUTING}. YEAR = {2013}}

In this work we specify various parameters like 1) local quantumness 2) entangling capability 3) classical randomness and give a canonical rep- representation of two qubit mixed quantum states based on them. Here we investigate the correlating capability of a non local Hamiltonian acting on general two qubit states in context of these parameters. In particular we address the questions like: 1.What is the rate of change of the standard measures of correlation like Entanglement (E) and Discord (D). 2.How these measures get affected by the change of the parameters. 3.For what choice of initial parameters, these rates of change of correlation like dE/dt ; dD/dt are maximum. 4.We study its application on bistable and open systems. Our study and analysis are completely based on the mixed quantum states quite unlike to the previous investigations based on pure quantum states.

@inproceedings{bib_Inte_2012, AUTHOR = {V, Suresh Kumar N and U, Deva Priyakumar and Singh, Harjinder and Roy, Saumya and Chakraborty, Tushar Kanti }, TITLE = {Inter- versus intra-molecular cyclization of tripeptides containing tetrahydrofuran amino acids: a density functional theory study on kinetic control}, BOOKTITLE = {Journal of Molecular Modeling}. YEAR = {2012}}

: Density functional B3LYP method was used to investigate the preference of intra and intermolecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.

@inproceedings{bib_Pref_2012, AUTHOR = {V, Suresh Kumar N and Singh, Harjinder and Pulukuri, Kiran Kumar and Chakraborty, Tushar K }, TITLE = {Preferential heterochiral cyclic trimerization of 5-(aminoethyl)-2- furancarboxylic acid (AEFC) driven by non-covalent interactions}, BOOKTITLE = {Journal of Molecular Graphics and Modelling}. YEAR = {2012}}

Theoretical justication for preferential heterochiral cyclic trimerization of 5- (aminoethyl)-2-furancarboxylic acid (AEFC) is attempted using density functional theory (DFT) calculations. Results from explicit solvent assisted reaction pathways indicate greater stability of heterochiral cyclic tripeptides over their homochiral counterparts, contrary to ndings from gas phase and implicit solvent phase results. Pathways explored at M06/6- 31G(d,p) and MP2/6-31G(d,p) levels of theory show kinetic preference for heterochiral cy- clization. Analysis of optimized geometries reveals existence of strong hydrogen bonding interactions in the solvated heterochiral tripeptides. Thus, the ability of the cyclic tripep- tides to form strong noncovalent interactions increases with conversion of stereochemistry at one of its chiral centers from homo to heterochiral conformation. The resulting change in molecular symmetry facilitates the interacting sites to reorient such that the peptide can in- teract with a nucleophile from both the faces. This is further substantiated by computed IR spectra, NBO and AIM data. Additionally, justication for the stability of heterochiral cyclic tripeptides comes from molecular electrostatic potential and electron density surfaces. These studies show clearly that for the kind of systems presented here, gas phase or implicit sol- vent phase studies are inadequate in explaining realistic situations. Calculations with solvent molecules, even if a few only, are necessary to substantiate experimental observations.

@inproceedings{bib_Desi_2012, AUTHOR = {Sharma, Sitansh and Singh, Harjinder }, TITLE = {Design of optimal laser pulses to control molecular rovibrational excitation in a heteronuclear diatomic molecule}, BOOKTITLE = {Journal of Chemical Sciences}. YEAR = {2012}}

Optimal control theory in combination with time-dependent quantum dynamics is employed to design laser pulses which can perform selective vibrational and rotational excitations in a heteronuclear diatomic system. We have applied the conjugate gradient method for the constrained optimization of a suitably designed functional incorporating the desired objectives and constraints. Laser pulses designed for several excitation processes of the HF molecule were able to achieve predefined dynamical goals with almost 100% yield.

@inproceedings{bib_Theo_2012, AUTHOR = {V, Suresh Kumar N and Singh, Harjinder }, TITLE = {Theoretical Insights into Cyclic Trimerization of 5-(Aminoethyl)-2-Furancarboxylic Acid (AEFC) and Anion Binding Properties}, BOOKTITLE = {Theoritical Chemistry Symposium}. YEAR = {2012}}

Theoretical insights into homo versus heterochiral cyclic trimerization of 5-(aminoethyl)-2-furancarboxylic acid (AEFC) are provided based on density functional theory (DFT) calculations[1]. A comparison of pathways leading to cyclic trimerization explored at M06/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory indicates signicance of the M06 functional in determining the barrier heights. Kinetic preference for heterochiral cyclization is clearly observed from results obtained at M06/6-31G(d,p) level of theory. Structure analysis of geometries reveals existence of strong hydrogen bonding interactions in the solvated heterochiral tripeptides. Further support comes from IR spectra, NBO and AIM calculations, molecular electrostatic potential and electron density surfaces. Our study shows that for the kind of systems, calculations with solvent molecules, even if a few only, are sucient to substantiate experimental observations. Further study on anion binding anity of the peptides has revealed that while both homo and heterochiral cyclic tripeptides show equal electronic energies of interaction for a uoride ion in gas phase, the homochiral cyclic tripeptide shows relatively larger electronic energy of interaction for chloride and bromide ions ( 4 kcal/mol) compared to that shown by heterochiral cyclic tripeptide. In solvent phase, the peptides possess anity for uoride and chloride ions only. While, heterochiral cyclic peptide shows slightly larger interaction for uoride ion, anity of homochiral peptide for chloride ion is slightly larger than its heterochiral counterpart. Though the heterochiral cyclic tripeptide of AEFC is a stable product with high yield, anion recognition propensities are comparable to that of homochiral cyclic tripeptide.

@inproceedings{bib_Elec_2012, AUTHOR = {RAI, SANDHYA and Singh, Harjinder }, TITLE = {Electronic structure theory based study of proline interacting with gold nano clusters}, BOOKTITLE = {Mol Model}. YEAR = {2012}}

t Interaction between metal nanoparticles and biomolecules is important from the view point of developing and designing biosensors. Studies on proline tagged with gold nanoclusters are reported here using density functional theory (DFT) calculations for its structural, electronic and bonding properties. Geometries of the complexes are optimized using the PBE1PBE functional and mixed basis set, i. e., 6-311++G for the amino acid and SDD for the gold clusters. Equilibrium configurations are analyzed in terms of interaction energies, molecular orbitals and charge density. The complexes associated with cluster composed of an odd number of Au atoms show higher stability. Marked decrease in the HOMO-LUMO gaps is observed on complexation. Major components of interaction between the two moieties are: the anchoring N-Au and O-Au bond; and the non covalent interactions between Au and N-H or O-H bonds. The electron affinities and vertical ionization potentials for all complexes are calculated. They show an increased value of electron affinity and ionization potential on complexation. Natural bond orbital (NBO) analysis reveals a charge transfer between the donor (proline) and acceptor (gold cluster). The results indicate that the nature of interaction between the two moieties is partially covalent. Our results will be useful for further experimental studies and may be important for future application

@inproceedings{bib_Dete_2012, AUTHOR = {Padhi, Siladitya and Singh, Harjinder and Jameel, Shahid and U, Deva Priyakumar }, TITLE = {Determination of the Native Oligomeric State of Vpu, Transmembrane Protein from HIV-1, and its Ion Channel Activity}, BOOKTITLE = {Lipid-Protein Interactions in Membranes: Implications for Health and Disease}. YEAR = {2012}}

Vpu is an 81-residue protein encoded by human immunodeficiency virus type I (HIV-1) that facilitates viral release from host cells. The protein has a cytoplasmic domain and a helical transmembrane (TM) domain, of which the latter oligomerizes to form cation-specific ion channels. The number of TM domains that constitute the channel is still unclear, with experimental studies indicating the existence of a variety of oligomeric states. In this study, we have examined the possibility of Vpu to exist in tetra-, penta-, and hexameric states using comprehensive molecular dynamics (MD) simulations. By modeling the TM domain as an ideal α-helix, we carried out replica-exchange MD simulations in an implicit membrane environment for obtaining suitable starting structures, which were then subjected to extensive MD simulations in a fully hydrated lipid bilayer environment. The results show that the pentameric form is the most stable oligomeric state (the tetramer and hexamer models lose their initial channel-like structure), with helices in the pentamer being held together by strong van der Waals interactions. Hydrogen bonds between lipid headgroups and basic/hydrophilic residues on the protein are stronger in the pentamer than in the tetramer or the hexamer, indicating that these interactions might play a role in adhering the pentamer to the membrane. Free energy calculations using umbrella sampling technique have been performed to examine the potassium ion permeation through the pentameric pore. The results show a high free energy barrier corresponding to ion transport indicating weak ion channel activity in agreement with previous experimental biophysical studies.

@inproceedings{bib_A_th_2011, AUTHOR = {RAI, SANDHYA and V, Suresh Kumar N and Singh, Harjinder }, TITLE = {A theoretical study on interaction of proline with gold cluster}, BOOKTITLE = {Bulletin of Materials Science}. YEAR = {2011}}

Interaction of proline with gold cluster was studied using density functional theory (DFT). Two types of mixed basis sets UB3LYP/6-311++G LANL2MB and UB3LYP/6-311++G LANL2DZ were used for optimization of complex structures. Proline interacts with gold cluster either through one anchor bond, N-Au or an anchor bond O-Au associated with a non-conventional O-H…Au hydrogen bond. Among these interactions, higher tendency for interaction is seen with Au cluster through amide terminal. Natural bond orbital analysis (NBO) is used to substantiate the results.

@inproceedings{bib_Lase_2011, AUTHOR = {Sharma, Sitansh and Singh, Harjinder }, TITLE = {Laser pulse shaping for optimal control of multiphoton dissociation in a diatomic molecule using genetic algorithm optimization}, BOOKTITLE = {The Journal of Chemical Physics}. YEAR = {2011}}

We have applied genetic algorithm optimization for the design of laser pulses to control dissociation process in the ground electronic state of HF molecule, within the mathematical framework of optimal control theory. In order to design the experimentally feasible laser fields, we coded the small set of selected field parameters in the GA parameter space. Two types of pulses, one with fixed frequency components and the other having non-deterministic components have been designed. Optimized laser field obtained using this approach, possesses simple time and frequency structures. We show that the fields having non-deterministic frequency components lead to greater dissociation probability compared to the ones having deterministic frequency components.

@inproceedings{bib_Gene_2010, AUTHOR = {SHARMA, SITANSH and Singh, Harjinder and Balint-Kurti, Gabriel }, TITLE = {Genetic algorithm optimization of laser pulses for molecular quantum state excitation}, BOOKTITLE = {The Journal of Chemical Physics}. YEAR = {2010}}

Conventionally optimal control theory has been used in the theoretical design of laser pulses through the direct variation in the electric field of the laser pulse as a function of time. This often leads to designed laser pulses which contain a broad and seemingly arbitrary frequency structure that varies in time in a manner which may be difficult to realize experimentally. In contrast, the experimental design of laser pulses has used a genetic algorithm (GA) approach, varying only those laser parameters actually available to the experimentalist. We investigate in this paper the possibility of using GA optimization methods in the theoretical design of laser pulses to bring about quantum state transitions in molecules. This allows us to select only a small limited number of parameters to vary and to choose these parameters so that they correspond to those available to the experimentalist. In the paper we apply our methods to the vibrational-rotational excitation of the HF molecule. We choose a small limited number of frequencies and vary only the associated electric field amplitudes and pulse envelopes. We show that laser pulses designed in this way can lead to very high transition probabilities.

@inproceedings{bib_Ster_2010, AUTHOR = {Chakraborty, Tushar Kanti and V, Suresh Kumar N and Roy, Saumya and Dutta, Sumit Kumar and Kunwar, A C and Sridhar, B and Singh, Harjinder }, TITLE = {Stereochemical control in the structures of linear δ,α-hybrid tripeptides containing tetrahydrofuran amino acids}, BOOKTITLE = {Journal of Physical Organic Chemistry}. YEAR = {2010}}

Structural and electronic properties of diastereomers of tetrahydrofuran amino acids (TAA) derived tripeptide, Boc-TAA-Leu-Val-OMe, are studied using density functional theory. Predicted secondary folding patterns with hydrogen bonded pseudocycles of different sizes in peptides containing (2R,5S)-cis-TAA and (2S,5R)-cis-TAA are confirmed by detailed NMR studies of both, and single crystal X-ray analysis of the former. A novel unusual folding pattern emanating from three-centered hydrogen bond is found in peptide with (2R,5S)-cis relationship. Stereochemical control on the orientation of interacting sites is substantiated by structural analysis of the peptides. Using natural bonding orbital and atoms in molecules analyses, charge transfer interactions are analyzed.

@inproceedings{bib_Desi_2010, AUTHOR = {SHARMA, SITANSH and Singh, Harjinder and Harvey, Jeremy N. and , Gabriel G. Balint-Kurti }, TITLE = {Design of an infrared laser pulse to control the multiphoton dissociation of the Fe-CO bond in CO-heme compounds}, BOOKTITLE = {The Journal of Chemical Physics}. YEAR = {2010}}

Optimal control theory is used to design a laser pulse for the multiphoton dissociation of the Fe– CO bond in the CO-heme compounds. The study uses a hexacoordinated iron–porphyrin– imidazole–CO complex in its ground electronic state as a model for CO liganded to the heme group. The potential energy and dipole moment surfaces for the interaction of the CO ligand with the heme group are calculated using density functional theory. Optimal control theory, combined with a timedependent quantum dynamical treatment of the laser-molecule interaction, is then used to design a laser pulse capable of efficiently dissociating the CO-heme complex model. The genetic algorithm method is used within the mathematical framework of optimal control theory to perform the optimization process. This method provides good control over the parameters of the laser pulse, allowing optimized pulses with simple time and frequency structures to be designed. The dependence of photodissociation yield on the choice of initial vibrational state and of initial laser field parameters is also investigated. The current work uses a reduced dimensionality model in which only the Fe–C and C–O stretching coordinates are explicitly taken into account in the timedependent quantum dynamical calculations. The limitations arising from this are discussed in Sec. IV.

@inproceedings{bib_Inte_2010, AUTHOR = {RAI, SANDHYA and Singh, Harjinder }, TITLE = {Interaction of Amino acids with gold clusters}, BOOKTITLE = {Theoritical Chemistry Symposium}. YEAR = {2010}}

Quantum chemical calculations using density functional theory (DFT) were carried out on systems containing gold atoms attached to amino acids (Proline, Histidine and Arginine). Geometries of amino acids with gold cluster were optimized using the DFT-B3LYP approach. The mixed basis set were used keeping 6-311++G for the amino acid part and 3 dierent basis sets were used for the gold part, i. e., LANL2DZ, LANL2MB and SDD. A comparision of the results using dierent basis sets was made. The interaction between the two moieties has two major components: (a) the anchoring N-Au and O-Au bond and (b) the non covalent interactions between Au and N-H or O-H bonds. The results indicate that there is eective charge transfer from amino acid to the gold cluster. This was conrmed by the natural bond orbital (NBO) analysis. The NBO analysis was also done in order to calculate the charge transfer, natural population analysis (NPA), and Wiberg bond indices of the complexes. The studies also indicated that these bond are partially covalent.

@inproceedings{bib_A_Th_2009, AUTHOR = {SHARMA, PURSHOTAM and SHARMA, SITANSH and Mitra, Abhijit and Singh, Harjinder }, TITLE = {A Theoretical Study on Interaction of Small Gold Clusters Aun (n = 4, 6, 8) with xDNA Base Pairs}, BOOKTITLE = {Journal of Biomolecular Structure and Dynamics}. YEAR = {2009}}

xDNA constitutes a novel class of size expanded synthetic nucleic acids in which one of the bases of the base pairs is larger than the natural DNA bases. These expanded bases are called x-bases. In this paper, we investigate the hydrogen bonding characteristics and relevant molecular properties of model complexes (xAT)Aun, (xTA)Aun, (xGC)Aun, and (xCG)Aun (n = 4, 6, 8) consisting of xDNA base pairs and gold clusters, in order to study the nature of gold-xDNA binding. We offer detailed characterization of their different aspects, viz., structural, electronic and spectroscopic, effect of gold cluster size, aromaticity, and planarity using quantum mechanics based density functional theory (DFT). Significant charge transfer is seen between the gold clusters and x-base pairs. Gold complexation is found to affect the interbase hydrogen bonding in these complexes. In addition to anchor bonds, XHAu type of hydrogen bonding interactions are also found to contribute to the gold-base pair binding in these complexes.

@inproceedings{bib_Desi_2009, AUTHOR = {SHARMA, SITANSH and SHARMA, PURSHOTAM and Singh, Harjinder and Balint-Kurti, Gabriel }, TITLE = {Design of laser pulses for selective vibrational excitation of the N6-H bond of adenine and adenine-thymine base pair using optimal control theory}, BOOKTITLE = {Journal of Molecular Modeling}. YEAR = {2009}}

Time dependent quantum dynamics and optimal control theory are used for selective vibrational excitation of the N6-H (amino N-H) bond in free adenine and in the adenine-thymine (A-T) base pair. For the N6-H bond in free adenine we have used a one dimensional model while for the hydrogen bond, N6-H (A)...O4(T), present in the A-T base pair, a two mathematical dimensional model is employed. The conjugate gradient method is used for the optimization of the field dependent cost functional. Optimal laser fields are obtained for selective population transfer in both the model systems, which give virtually 100% excitation probability to preselected vibrational levels. The effect of the optimized laser field on the other hydrogen bond, N1(A)...H- N3(T), present in A-T base pair is also investigated.

@inproceedings{bib_Pref_2009, AUTHOR = {V, Suresh Kumar N and SHARMA, PURSHOTAM and Chakraborty, Tushar Kanti and Singh, Harjinder }, TITLE = {Preferential cyclization in tetrahydrofuran amino acids.}, BOOKTITLE = {Changing Paradigms in Theoretical & Computational Chemistry from atoms to molecular cluster}. YEAR = {2009}}

We provide theoretical insights for the observed preference of cyclodimerization over intramolecular cyclization reactions in tetrahydrofuran amino acid using high level DFT quantum chemical methods, in the gas phase as well as in continuum solvent medium. Thermodynamic results obtained from Hessian calculations indicate the higher stability of intermolecularly cyclized dimer over intramolecularly cyclized monomer. NBO and AIM analysis also support the existence of additional stabilizing hydrogen bond interactions in intermolecularly cyclized products. Further justification for the presence of stabilizing interactions in intermolecularly cyclized products comes from the molecular electrostatic potentials and electron density surfaces.

@inproceedings{bib_QUAN_2009, AUTHOR = {SHARMA, SITANSH and Singh, Harjinder and Balint-Kurti, Gabriel G. }, TITLE = {QUANTUM OPTIMAL CONTROL OF NUCLEAR MOTION AND PHOTODISSOCIATION USING GENETIC ALGORITHM}, BOOKTITLE = {Changing Paradigms of Theoretical and Computational Chemistry: From Atoms to Molecular Clusters}. YEAR = {2009}}

Conventionally optimal control theory [1, 2, 3] has been used in the theoretical design of laser pulses through the direct variation of the electric field of the laser pulse as a function of time. This often leads to designed laser pulses which contain a broad and seemingly arbitrary frequency structure that varies in time in a manner which may be difficult to realize experimentally. In contrast, in Genetic Algorithm (GA) approach, a few control parameters are used, which are actually available to the experimentalist. In this work, we investigate the possibility of using GA optimization methods in the theoretical design of laser pulses to bring about quantum state transitions in molecules. This allows us to select only a small limited number of parameters to vary and to choose these parameters so that they correspond to those available to the experimentalist. In this work, we apply our methods to the vibrational-rotational excitation of the HF molecule. We choose a small limited number of frequencies and vary only the associated electric field amplitudes and pulse envelopes. We show that laser pulses designed in this way can lead to very high transition probabilities. The mechanism of population transfer during the excitation process is investigated by projecting the laser driven nuclear wave function onto the eigenstates of the system. We have also investigated the possibility of photodissociation of HF molecule by climbing up the vibrational ladder using this genetic algorithm approach.

@inproceedings{bib_Quan_2009, AUTHOR = {Sharma, Sitansh and Singh, Harjinder and G, Gabriel and Balint-Kurti, }, TITLE = {Quantum dynamics and optimal control of nuclear motion in the hydrogen bonds of adenine-thymine DNA base pair}, BOOKTITLE = {International Conference on Physics Biology Interface}. YEAR = {2009}}

Quantum optimal control theory along with time dependent quantum dynamics is used to control the nuclear motion in the hydrogen bonds of adenine-thymine (A-T) DNA base pair [1]. Optimal infrared laser pulses are designed for selective excitations of (a) single N-H O hydrogen bond and (b) both N-H O and N-H N bonds simultaneously. The conjuagte gradient method is employed to optimize the constructed eld dependent grand functional. Optimal laser elds are realized which give more than 99% population transfer to the preselected vibrational states. The mechanism of population transfer during the vibrational excitation process is investigated by projecting the laser driven nuclear wavefunction onto the vibrational states of the system.

@inproceedings{bib_Elec_2009, AUTHOR = {V, Suresh Kumar N and Singh, Harjinder and Chakraborty, Tushar K. }, TITLE = {Electronic structure based study of furan derived peptides}, BOOKTITLE = {Of Molecules and Materials}. YEAR = {2009}}

Cyclic peptides incorporating a 5 membered ring such as furan mimic naturally occurring cyclic peptides[1]. The preferred conformation of linear and cyclic tripeptides incorporating such sugar amino acids depends on the stereochemistry at the chiral center. Control of stereochemistry at C position of amino ethyl furan carboxylic acid (AEFC) unit in the linear and cyclic tripeptides is investigated using structural parameters and energetics data obtained from density functional theory (DFT) based calculations at B3LYP/6-31G(d,p) level of theory. We found that R-isomer of AEFC unit prefers to form bond with its S-isomer. Thermodynamic analysis revealed that linear tripeptide formed by two R-configured isomers of AEFC and one S-configured isomer of AEFC (RRS or RSR linear) is more stable than that formed by three R-configured isomers of AEFC (RRR linear). It is found that the cyclic tripeptide formed by two R-configured isomers of AEFC and one S-configured isomer of AEFC, i. e., cyclic RRS product is formed with high yield than that formed by three R-configured isomers of AEFC (RRR cyclic) though cyclic RRR trimer is more stable than cyclic RRS trimer. This is substantiated by kinetic control of reactions leading to cyclic tripeptides from linear tripeptides. Using NBO analysis stabilizing interactions in all the linear and cyclic tripeptides are identified. Molecular electrostatic potential (MESP) surfaces of cyclic tripeptides provide insights of intramolecular hydrogen bond interactions. The MESP mapped electron density surfaces have shown the charge distribution around the cyclic peptides.

@inproceedings{bib_Elec_2009, AUTHOR = {V, Suresh Kumar N and Singh, Harjinder and Chakraborty, Tushar K }, TITLE = {Electronic structure and properties based study of furan and tetrahydrofuran derived peptides}, BOOKTITLE = {Changing Paradigms in Theoretical & Computational Chemistry from atoms to molecular cluster}. YEAR = {2009}}

Peptides incorporating 5 membered rings such as furan and tetrahydrofuran (THF) adopt secondary folding patterns and thus mimic natural peptides. The preferred conformation of linear and cyclized peptides incorporating sugar amino acids depends on the stereochemistry of at the chiral center. Control of stereochemistry of THF amino acid (TAA) in the structure of the linear tripeptide Boc-TAA-Leu-Val-OMe containing (2R,5S)-cis TAA, (2S,5R)-cis TAA, (2R,5R)-trans TAA and (2S,5S)-trans TAA is investigated using structural parameters and energetics data obtained from density functional theory (DFT) based calculations at B3LYP/6-31G(d,p) level of theory. We found that the conformations associated with -, - turn structures are stabilized by intramolecular hydrogen bonding interactions. Kinetic control of reactions leading to intra and inter molecular cyclization of tripeptide TAA-Gly-Gly containing (2S,5R)-cis TAA and (2S,5S)-trans TAA is studied at the same level of theory in gas phase[1]. We observe that kinetic control favors cyclodimerization instead of intramolecular cyclization. Theoretical study of reactions leading to linear and cyclic trimerization of backbone altered -peptide, i. e., amino ethyl furan carboxylic acid (AEFC) at the same level of theory have revealed the role of stereochemistry at C position of AEFC in the preferential formation of asymmetric RRS cyclic tripeptide formed by R-, R- and S- stereo isomers of AEFC.

@inproceedings{bib_Quan_2009, AUTHOR = {V, Suresh Kumar N and U, Deva Priyakumar and Singh, Harjinder and Chakraborty, T. K. }, TITLE = {Quantum chemical study of control of stereochemistry of tetrahdyrofuran ring in tripeptides containing tetrahydrofuran amino acids}, BOOKTITLE = {International Conference on Physics Biology Interface}. YEAR = {2009}}

Design of biomimetic systems is an alternative method of finding biologically active molecules. Peptides incorporating tetrahydrofuran amino acids (TAA) adopt secondary folding patterns and thus mimic natural peptides. The preferred conformation of TAA derived linear and cyclized peptides depends on the stereochemistry of the tetrahydrofuran (THF) ring. Control of stereochemistry of THF ring in the structure of the linear tripeptide Boc-TAA-Leu-Val- OMe containing (2R,5S)-cis TAA, (2S,5R)-cis TAA, (2R,5R)-trans TAA and (2S,5S)-trans TAA is investigated using structural parameters and energetics data obtained from density functional theory (DFT) based calculations at B3LYP/6-31G(d,p) level of theory. We found that the conformations associated with -, -turn structures are stabilized by intramolecular hydrogen bonding interactions. Kinetic control of reactions leading to intra and inter molecular cyclization of tripeptide TAA-Gly-Gly containing (2S,5R)-cis TAA and (2S,5S)-trans TAA is studied at the same level of theory in gas phase.[1] We observe that kinetic control favors cyclodimerization instead of intramolecular cyclization.

@inproceedings{bib_ab_i_2008, AUTHOR = {SHARMA, PURSHOTAM and SHARMA, SITANSH and Singh, Harjinder and Mitra, Abhijit and Bhattacharyya, Dhananjay }, TITLE = {ab initio quantum mechanical studies of a pH dependant G:G conformational switch}, BOOKTITLE = {International Conference on Bioinformatics and Drug Discovery, Bioconvene}. YEAR = {2008}}

Identification of base pairs which can participate, through multimodality of edge interactions, in conformational switching events, and evaluation of possible environmental factors responsible for the switching can lead to greater understanding of RNA functional dynamics. Moleculardynamics studies by Schneider et al involving multimodality in C:U W:W cis interactions in aqueous medium, arguments forwarded by Van Dongen et al in support of a pH dependent G:C W:W cis to G:C H:W cis conformational switch and the postulation of putative role of a minor motifs in ribosomal dynamics through structure analysis, are examples of efforts in this section. Here we discuss the computational analysis of a putative pH dependant conformational switching of G:G base pairs in RNA structures.

@inproceedings{bib_Inte_2008, AUTHOR = {SHARMA, PURSHOTAM and SHARMA, SITANSH and Singh, Harjinder and Mitra, Abhijit }, TITLE = {Interaction of size expanded DNA bases with small neutral gold nano clusters}, BOOKTITLE = {International Nanoelectronics Conference}. YEAR = {2008}}

In this paper, we have computationally described the interaction of yDNA bases with small gold clusters through a variety of aspects including geometrical, spectroscopic and energetic one. To get insights in to essential elements of this interaction, the contribution of typical energy interaction components have also been investigated.

@inproceedings{bib_Vibr_2008, AUTHOR = {Singh, Harjinder }, TITLE = {Vibrational control of molecular systems in simple and complex environments}, BOOKTITLE = {The Electronic Structure and Properties of Atoms and Molecules}. YEAR = {2008}}

Controlling dynamics at the atomic level is a primary goal of chemists. In the last decade, Optimal control theory (OCT) has emerged as one comprehensive means of designing laser pulses for achieving prescribed dynamical goals. We have used OCT to obtain infrared laser pulses for the selective vibrational excitation of several different systems, from a simple diatomic to triatomic systems located in complex molecular environments. We will present our results obtained for the diatomic system HF applying OCT using different algorithmic methods, namely an iterative method, conjugate gradient method and genetic algorithms. The results of a new dynamic method for applying the penalty term needed to keep the power in the electric field of the laser within reasonable bounds will be discussed. For the triatomic FeCO, we use a two mathematical dimensional model of carboxy-myoglobin. Density functional theory is used to obtain the potential energy and dipole moment surfaces of the active site model. The Conjugate gradient method is employed to optimize the cost functional and to obtain the optimized laser pulses. Optimized laser fields are found which give virtually 100% excitation probability to preselected vibrational levels. Similar application to hydrogen bonding in a complex system will also be presented.

@inproceedings{bib_Elec_2008, AUTHOR = {SINGH, HIMANSHU and SHARMA, PURSHOTAM and Singh, Harjinder }, TITLE = {Electronic structure studies of DNA-nanoclusters}, BOOKTITLE = {National Biennial Conference of Nanosciences and Nanotechnology}. YEAR = {2008}}

The synthesis of modified versions of DNA is an area that is receiving much attention because of their potential applications in biotechnology and nanotechnology. Recently, Eric Kool et al have re-engineered an expanded version of DNA by pairing size expanded x-bases with normal bases in a complementary manner, which they called as xDNA. xDNA bases are analogues of natural bases that are formed by insertion of benzene ring into the natural bases. Recently, there was arisen a huge interest in conducting properties of metal bound DNA structures. We use quantum chemistry methods to investigate the structural and electronic properties of x-bases and their interaction with gold atoms, in order to explore develop insight into the nature of binding between gold atoms and size expanded DNA.

@inproceedings{bib_Stru_2008, AUTHOR = {SMITA, MADHU and Singh, Harjinder and Mitra, Abhijit and Karlapalem, Kamalakar }, TITLE = {Structure Simulation of Pentapeptide with Real valued Genetic Algorithm}, BOOKTITLE = {International Conference on Bioinformatics and Drug Discovery, Bioconvene}. YEAR = {2008}}

The problem of predicting the 3D native conformation of a polypeptide given the primary sequence is of fundamental importance in contemporary biology. Here we present a novel Genetic algorithm method to obtain the optimal geometry of a pentapeptide. The pentapeptide moiety is found in wide set of configurations in protein databases. A genetic algorithm utilizes optimization procedure similar to natural genetic evolution. Unlike other genetic algorithms, which are constrained to operate on bit strings, the algorithm used here operates on real values. A random population of conformations is generated taking into account the constraints of Ramachandran plot. This population advances through successive generations in which the solutions evolve via genetic operators (Mutate, Variate and Crossover); in such a way that it gives both better survival chance to fitter soluctions and a larger diversity within the population. More attention will be given to favorable local structures while unfavorable local structures will be rapidly abandoned on the basis of their fitness functions (potential energy), which are calculated using the GROMOS-96 force field of Spdbv version-3.7. The SCWRL3.0 program developed at Dunbrack lab is used for placing side chains to a fixed backbone coordinates. This algorithm proved to be very efficient for the penta-peptide Met-Enkephalin, a natural Opioid polypeptide produced in the brain. The algorithm converged only in 41 minutes and in 23 generations keeping the population size fixed (20 individual per population). The converged structure is energetically as stable as the native conformation of the protein. Its shows a RMSD of 5.9 from the original native conformation.

@inproceedings{bib_Stat_2008, AUTHOR = {Singh, Harjinder }, TITLE = {State of the art quantum chemical calculations of structures and properties of medium sized molecular systems}, BOOKTITLE = {Modern Trends in Chemistry: Molecules to Material}. YEAR = {2008}}

With availability of fast computers, electronic structure and properties calculations of small to medium sized systems using quantum chemical methods are now commonplace. Several options in addition to obtaining structures with energy optimisation are now easily realisable, e.g., carrying out calculations of electrostatic potential interations, atoms in molecule approach of Bader, Natural Bonding orbital method, etc. We discuss results obtained in specific cases using these options. We have recently carried out studies on several such systems including amino-methyl furan carboxylic acid system and binding of gold nanoclusters with size expanded DNA bases, xA, xC, xG, and xT. We will present the motivation behind such works and discuss the results obtained using different methods. Geometries of these molecular systems were fully optimized using the Hartree Fock SCF method and using B3LYP density functional method (DFT). The calculations provide a theoretical understanding beyond a phenomenological observation of the preferential cyclotrimerization of 5- (aminomethyl)-2-furancarboxylic acid (AMFC). Other than calculations of thermodynamic free energy, a detailed analysis of the molecular properties is carried out. The electrostatic potentials (ESP) in the region around molecular skeletons are investigated to provide justication for the preferential formation of the cyclic tripeptide over the cyclic dipeptide from the building block, AMFC. The ESP are calculated and computed on the molecular surfaces of the oligopeptides. There are repulsions observed in the dimer due to the proximity of the ethereal oxygen atoms of the furan rings. Natural bond orbital (NBO) analysis is done to find the second-order interactions, and atoms in molecules (AIM) calculations are performed to explore the interactions between the donor and acceptor moieties in the molecule. Our results on the gold complexed x-bases show that the gold clusters around xA and xT adopt triangular geometries, whereas irregular structures are obtained in the case of gold clusters complexed around xC and xG. The lengths of the bonds between atoms in the x-bases increase on gold complexation. The aromaticcharacter of the x-bases also increases on gold complexation except for the five member rings. A significant charge transfer from the x-base to gold atoms is seen in these complexes. Second-order interactions are observed in addition to direct covalent bonds between gold atoms and x bases.

@inproceedings{bib_Desi_2008, AUTHOR = {Singh, Harjinder and SHARMA, SITANSH and KUMAR, T. PRAVEEN and Harvey, Jeremy N. and Balint-Kurti, Gabriel G. }, TITLE = {Design of Optimal Laser fields to control vibrational excitations in Carboxy-myoglobin}, BOOKTITLE = {Proceedings of International Conference of Computer Science}. YEAR = {2008}}

The last two decades have seen increasing interest in the area of controlling dynamics at the atomic level. Among the several approaches used, Optimal Control Theory (OCT) has emerged as a powerful method for designing laser pulses to achieve prescribed dynamical goals. We have used OCT to obtain infrared laser pulses for the selective vibrational excitation of several different systems, from a simple diatomic to triatomics located in complex molecular environments. We use time dependent quantum mechanics to monitor the evolution of the system subject to a varying laser field. We have obtained fields for vibrational control of the diatomic system HF applying OCT using different algorithms, namely an iterative method, conjugate gradient method and genetic algorithms. The time-dependent quantum mechanical propagation of the system is achieved using the split operator form of the time evolution operator together with Fast Fourier transforms and grid methods. For the modelling of FeCO in carboxy-myoglobin, we use a two mathematical dimensional model. Density functional theory is used to obtain the potential energy and dipole moment surfaces of the active site model, while the conjugate gradient method is employed within the OCT optimization procedure to obtain the laser pulses. Optimized laser fields are found which give virtually 100% excitation probability to preselected vibrational levels. A similar application to a hydrogen bonded system of biological significance will also be presented. In all cases, detailed analyses of the field are carried out in terms of its power spectrum and the time variation of the contributions from the frequencies involved.

@inproceedings{bib_Vari_2008, AUTHOR = {SMITA, MADHU and Mitra, Abhijit and Singh, Harjinder }, TITLE = {Variation of conformational propensity of different amino acids within disallowed and allowed regions of the Ramachandran Plot}, BOOKTITLE = {International Conference on Bioinformatics and Drug Discovery, Bioconvene}. YEAR = {2008}}

The backbone conformation of amino acids in proteins is represented mainly by two torsion angles; phi and psi. Ramachandran map is a way to visualize these torsion angles in protein structures. Here we analyze the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in protein structures. A non redundant data set consisting of 405 high resolution protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 78,213 non-Gly residues, which were characterized on the basis of their backbone dihedral angles phi and psi. Residues falling outside the defined "broad allowed limits" on the Ramachandran map were analyzed. The results suggested that very small fraction of residues (approximately 0.4%) lie in appreciably disallowed regions. Interestingly, small polar/charged residues showed significantly greater probability of adopting unusual backbone with the largest number of examples being observed for Asn, Asp, Ser and Thr residues. The bulky charged residues Glu, Lys, Gln and Arg have a relatively low propensity for backbone distortions. Bulky hydrophobic residues which are found predominantly in well packed interiors of proteins like Ile, Val and aromatic amino acids like Phe, Trp and Tyr do not generally adopt disallowed conformations. In the allowed region irrespective of the type of amino acid except Gly, there is a high propensity for phi value of the range -70 to -60 and for psi value 140 to 150.

@inproceedings{bib_Nonc_2008, AUTHOR = {SHARMA, PURSHOTAM and Singh, Harjinder and Mitra, Abhijit }, TITLE = {Noncanonical Base pairing in RNA: Topological and NBO analysis of Hoogsteen edge : Sugar edge interactions}, BOOKTITLE = {INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE}. YEAR = {2008}}

Hoogsteen-sugar base pattern of RNA base pairing is studied using density functional theory. Hydrogen bonding patterns of these base apirs are characterized using NBO analysis and AIM analysis. Correlation between strenghth of base pairing and nature of donor-acceptor combinations is also carried out.

@inproceedings{bib_Real_2008, AUTHOR = {SMITA, MADHU and Mitra, Abhijit and Singh, Harjinder }, TITLE = {Real Valued Genetic Algorithm Based Approach for Protein Structure Prediction - Role of Biophysical Filters for reduction of Conformational Search Space}, BOOKTITLE = {International Conference on Pattern Recognition in Bioinformatics}. YEAR = {2008}}

Predicting the 3D native conformation of a protein given the amino acid sequence is known as protein structure prediction (PSP)problem and is one of the greatest challenge of computational biology. The current work uses a real valued Genetic Algorithm (GA), a powerful variant of conventional GA to simulate the PSP problem. It consists of three evolutionary operators to manipulate the genes and a fitness function based on a simple force field. The individuals of the population correspond to different conformations of the same polypeptide chain, represented by a string of (phi,psi)torsion angles. The conformations are generated under the constraints of Ramachandran plot along with secondary structure information, which are then screened through a set of knowledge based biophysical filters, viz. persistence length and radius of gyration. Only the structures satisfying the filtering criteria are considered for energy minimization using GA. The algorithm has been validated on a set of known globular protein containing 2-4 secondary structure elements. For all the test proteins the algorithm converges rapidly ad the converged structure shows a backbone RMSD (root mean square deviation) or 3-6A as compared to the native structure.

@inproceedings{bib_Cont_2007, AUTHOR = {KUMAR, B PRAVEEN and Singh, Harjinder }, TITLE = {Controlling dynamics in diatomic systems}, BOOKTITLE = {Journal of Chemical Sciences}. YEAR = {2007}}

Controlling molecular energetics using laser pulses is exemplified for nuclear motion in two different diatomic systems. The problem of finding the optimized field for maximizing a desired quantum dynamical target is formulated using an iterative method. The method is applied for two diatomic sys- tems, HF and OH. The power spectra of the fields and evolution of populations of different vibrational states during transitions are obtained.

@inproceedings{bib_Bind_2007, AUTHOR = {SHARMA, PURSHOTAM and SINGH, HIMANSHU and SHARMA, SITANSH and Singh, Harjinder }, TITLE = {Binding of gold Nanoclusters with size-expanded DNA bases: A computational study of structural and electronic properties}, BOOKTITLE = {Journal of Chemical Theory and Computation}. YEAR = {2007}}

Binding of Gold Nanoclusters with Size-Expanded DNA Bases: A Computational Study of Structural and Electronic Properties Purshotam Sharma, Himanshu Singh, Sitansh Sharma, and Harjinder Singh* Center for Computational Natural Sciences and Bioinformatics, International Institute of Information and Technology, Gachibowli, Hyderabad-500032, India Received June 15, 2007 Abstract: Binding of gold nanoclusters with size-expanded DNA bases, xA, xC, xG, and xT, is studied using quantum chemical methods. Geometries of the neutral xA-Au6, xC-Au6, xG-Au6, and xT-Au6 complexes were fully optimized using the B3LYP density functional method (DFT). The gold clusters around xA and xT adopt triangular geometries, whereas irregular structures are obtained in the case of gold clusters complexed around xC and xG. The lengths of the bonds between atoms in the x-bases increase on gold complexation. The aromatic character of the x-bases also increases on gold complexation except for the five-member rings. A significant charge transfer from the x-base to gold atoms is seen in these complexes. Second-order interactions are observed in addition to direct covalent bonds between gold atoms and x-bases.

@inproceedings{bib_Quan_2007, AUTHOR = {SHARMA, SITANSH and SHARMA, PURSHOTAM and Singh, Harjinder }, TITLE = {Quantum control of vibrational excitations in a heteronucler diatomic molecule}, BOOKTITLE = {Journal of Chemical Sciences}. YEAR = {2007}}

Optimal control theory is applied to obtain infrared laser pulses for selective vibrational excitation in a heteronuclear diatomic molecule. The problem of finding the optimized field is phrased as a maximization of a cost functional which depends on the laser field. A time dependent Gaussian factor is introduced in the field prior to evaluation of the cost functional for better field shape. Conjugate gradient method21,24 is used for optimization of constructed cost functional. At each instant of time, the optimal electric field is calculated and used for the subsequent quantum dynamics, within the dipole approximation. The results are obtained using both Morse potential as well as potential energy obtained using ab initio calculations.

@inproceedings{bib_Enth_2007, AUTHOR = {Rudra, Shalini Gaur and Singh, Harjinder and Basu, Santanu and Shivhare, U S }, TITLE = {Enthalpy entropy compensation during thermal degradation}, BOOKTITLE = {Journal on Food Engineering}. YEAR = {2007}}

Enthalpy entropy compensation effect has been a debatable topic for explaining the thermodynamic parameters in chemical reactions. Kinetic data for thermal degradation of chlorophylls (a, b and total) at 105145 C in coriander and mint leaf puree at pH 5.58.5 was used for this study. By applying the modified transition state theory and Krugs unbiased statistical regression procedure, the existence of thermodynamic compensation was tested for chlorophyll degradation. Enthalpy of activation (DH) for the coriander and mint purees ranged from 2.36 to 91.99 kJ/mol while entropy (DS) ranged from 0.047 to 0.713 kJ/(mol K). Though the enthalpy and entropy val- ues exhibited an excellent linear relationship (R2> 0.96), a critical analysis of the results indicated absence of any extra-thermodynamic effect or thermodynamic compensation for chlorophylls degradation. The presence of isokinetic point was also not detected.

@inproceedings{bib_Base_2007, AUTHOR = {Mitra, Abhijit and Singh, Harjinder and SHARMA, PURSHOTAM and SHARMA, SITANSH }, TITLE = {Base pairing in RNA structures: A computational analysis of structural aspects and interactions energies}, BOOKTITLE = {Journal of Chemical Sciences}. YEAR = {2007}}

Abstract. The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G** level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. The dipole moments of the bases are reduced on full optimization. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.

@inproceedings{bib_Quan_2007, AUTHOR = {Mitra, Abhijit and Singh, Harjinder and SHARMA, PURSHOTAM and SHARMA, SITANSH and Bhattacharyya, Dhananjay }, TITLE = {Quantum Chemical Studies of Structures and binding in Noncanonical RNA Base pairs: The Trans Watson Crick/Watson-Crick family}, BOOKTITLE = {Journal of Biomolecular Structure and Dynamics}. YEAR = {2007}}

Abstract The trans Watson-Crick/Watson-Crick family of base pairs represent a geometric class which play important structural and possible functional roles in the ribosome, tRNA and other functional RNA molecules. They nucleate base triplets and quartets, participate as loop closing terminal base pairs in hair pin motifs and are also responsible for several tertiary interactions which enable sequentially distant regions to interact with each other in. Eleven representative examples spanning nine systems belonging to this geometric family of RNA base pairs, having widely different occurrence statistics in the PDB database, were studied at the HF/6-31G (d, p) level using Morokuma decomposition, Atoms in Molecule as well as Natural Bond Orbital methods in the optimized gas phase geometries and in their crystal structure geometries respectively. The BSSE and deformation energy corrected interaction energy values for the optimized geometries for non protonated base pairs ranged from -8.19 kcal/mol to -21.84 kcal/mol and compared favorably with those of canonical base pairs. The interaction energies of these base pairs, in their respective crystal geometries, were however lesser to varying extents and in one case, that of A:A W:W trans, it was actually found to be positive. The variation in RMSD between the two geometries was also large and ranged from 0.32 2.19 . Our analysis shows that the hydrogen bonding characteristics and interaction energies obtained, correlated with the nature and type of hydrogen bonds between base pairs; but the occurrence frequencies, interaction energies and geometric variabilities were conspicuous by the absence of any apparent correlation. Instead, the functional geometry of base pairs and the nature of their local interaction energy hyperspace, in conjunction with tertiary and neighboring group interaction potentials in the global context, could be correlated with the identities of free and bound hydrogen bond donor/acceptor groups present in interacting bases. It also suggests that the concept of isostericity alone may not always determine covariation potentials for base pairs, particularly those which may be participating in functional dynamics. These considerations are more important than the absolute values of the interaction energies in their respective optimized geometries in rationalizing their occurrences in functional RNAs. They highlight the importance of revising some of the existing DNA based structure analysis approaches and may have significant implications for RNA structure and dynamics, especially in the context of structure prediction algorithms.