Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions

In this article, we present a novel application of a quantum clustering (QC) technique to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. We further portray each conformational population in terms of dynamically stable network parameters which beautifully capture the ligand induced variations in the ensemble in atomistic detail. The conformational populations thus identified by the QC method and verified by network parameters are evaluated for different ligand bound states of the protein pyrrolysyl-tRNA synthetase (DhPylRS) from D. hafniense. The ligand/environment induced re-distribution of protein conformational ensembles forms the basis for understanding several important biological phenomena such as allostery and enzyme catalysis. The atomistic level characterization of each population in the conformational ensemble in terms of the re-orchestrated networks of amino acids is a challenging problem, especially when the changes are minimal at the backbone level. Here we demonstrate that the QC method is sensitive to such subtle changes and is able to cluster MD snapshots which are similar at the side-chain interaction level. Although we have applied these methods on simulation trajectories of a modest time scale (20 ns each), we emphasize that our methodology provides a general approach towards an objective clustering of large-scale MD simulation data and may be applied to probe multistate equilibria at higher time scales, and to problems related to protein folding for any protein or protein-protein/RNA/DNA complex of interest with a known structure.

Subquadratic quantum number dependence and other anomalies of vibrational dephasing in liquid nitrogen: Molecular dynamics simulation study from the triple point to the critical point and beyond

Vibrational phase relaxation near gas-liquid and liquid-solid phase coexistence has been studied by molecular dynamics simulations of N-N stretch in N-2. Experimentally observed pronounced insensitivity of phase relaxation from the triple point to beyond the boiling point is found to originate from a competition between density relaxation and resonant-energy transfer terms. The sharp rise in relaxation rate near the critical point (CP) can be attributed at least partly to the sharp, rise in vibration-rotation coupling contribution. Substantial subquadratic quantum number dependence of overtone dephasing rate is found near the CP and in supercritical fluids. [S0031-9007 (99)09318-7].

Quantum theoretical study of molecular mechanisms of mutation and cancer - A review

Several endogenous and exogenous chemical species, particularly the so-called reactive oxygen species (ROS) and reactive nitrogen oxide species (RNOS), attack deoxyribonucleic acid (DNA) in biological systems producing DNA lesions which hamper normal cell functioning and cause various diseases including mutation and cancer. The guanine (G) base of DNA among all the bases is most susceptible and certain modified guanines get involved in mispairing with other bases during DNA replication. The biological system repairs the abnormal base pairs, but those that are still left cause mutation and cancer. Anti-oxidants present in biological systems can scavenge the ROS and RNOS. Thus three types of molecular events occur in biological media: (i) DNA damage, (ii) DNA repair, and (iii) prevention of DNA damage by scavenging ROS and RNOS. Quantum mechanical methods may be used to unravel molecular mechanisms of such phenomena. Some recent quantum theoretical results obtained on these problems are reviewed here.

Developments in quantum information processing by nuclear magnetic resonance: Use of quadrupolar and dipolar couplings

Use of dipolar and quadrupolar couplings for quantum information processing (QIP) by nuclear magnetic resonance (NMR) is described. In these cases, instead of the individual spins being qubits, the 2(n) energy levels of the spin-system can be treated as an n-qubit system. It is demonstrated that QIP in such systems can be carried out using transition-selective pulses, in (CHCN)-C-3, (CH3CN)-C-13, Li-7 (I = 3/2) and Cs-133 (I = 7/2), oriented in liquid crystals yielding 2 and 3 qubit systems. Creation of pseudopure states, implementation of logic gates and arithmetic operations (half-adder and subtractor) have been carried out in these systems using transition-selective pulses.

Implementation of conditional phase-shift gate for quantum information processing by NMR, using transition-selective pulses

Experimental realization of quantum information processing in the field of nuclear magnetic resonance (NMR) has been well established. Implementation of conditional phase-shift gate has been a significant step, which has lead to realization of important algorithms such as Grover's search algorithm and quantum Fourier transform. This gate has so far been implemented in NMR by using coupling evolution method. We demonstrate here the implementation of the conditional phase-shift gate using transition selective pulses. As an application of the gate, we demonstrate Grover's search algorithm and quantum Fourier transform by simulations and experiments using transition selective pulses. (C) 2002 Elsevier Science (USA). All rights reserved.

Quantum spin models with exact dimer ground states

Inspired by the exact solution of the Majumdar-Ghosh model, a family of one-dimensional, translationally invariant spin Hamiltonians is constructed. The exchange coupling in these models is antiferromagnetic, and decreases linearly with the separation between the spins. The coupling becomes identically zero beyond a certain distance. It is rigorously proved that the dimer configuration is an exact, superstable ground-state configuration of all the members of the family on a periodic chain. The ground state is twofold degenerate, and there exists an energy gap above the ground state. The Majumdar-Ghosh Hamiltonian with a twofold degenerate dimer ground state is just the first member of the family. The scheme of construction is generalized to two and three dimensions, and illustrated with the help of some concrete examples. The first member in two dimensions is the Shastry-Sutherland model. Many of these models have exponentially degenerate, exact dimer ground states.

Solid state structural and solution studies on the formation of a flexible cavity for anions by copper(I) and 1,2-bis(diphenylphosphino)ethane

Copper(l) complexes of 1,2-bis(diphenylphosphino)ethane (dppe) with a stoichiometry Cu-2(dppe)(3)(X)(2) [X- = CN- (1), SCN- (2), NO3- (3)] are obtained from direct reactions of CuX and dppe. The complexes are structurally and spectroscopically (NMR and IR) characterized. The structure of the [Cu-2(dPPe)(3)](2+) dication is similar to the structural motif observed in many other complexes with a chelating dppe and a bridging dppe connecting two copper centers. In complexes 1 -3, the anions are confined to the cavity formed by the phosphines which force a monodentate coordination mode despite the predominant bidentate/bridging character of the anions. The coordination angles rather than the thermochemical radii dictate the steric requirement of anions. While the solution behavior of 3, with nitrate, is similar to complexes studied earlier, complexes with pseudohalides exhibit new solution behavior. (C) 2002 Elsevier Science Ltd. All rights reserved.

Grain Floatation During Equiaxed Solidification of an Al-Cu Alloy in a Side-Cooled Cavity: Part II-Numerical Studies

In this article, a single-phase, one-domain macroscopic model is developed for studying binary alloy solidification with moving equiaxed solid phase, along with the associated transport phenomena. In this model, issues such as thermosolutal convection, motion of solid phase relative to liquid and viscosity variations of the solid-liquid mixture with solid fraction in the mobile zone are taken into account. Using the model, the associated transport phenomena during solidification of Al-Cu alloys in a rectangular cavity are predicted. The results for temperature variation, segregation patterns, and eutectic fraction distribution are compared with data from in-house experiments. The model predictions compare well with the experimental results. To highlight the influence of solid phase movement on convection and final macrosegregation, the results of the current model are also compared with those obtained from the conventional solidification model with stationary solid phase. By including the independent movement of the solid phase into the fluid transport model, better predictions of macrosegregation, microstructure, and even shrinkage locations were obtained. Mechanical property prediction models based on microstructure will benefit from the improved accuracy of this model.

Grain Floatation During Equiaxed Solidification of an Al-Cu Alloy in a Side-Cooled Cavity: Part I-Experimental Studies

Experimental studies were performed to investigate the role and influence of grain movement on macrosegregation and microstructure evolution during equiaxed solidification. Casting experiments were performed with a grain-refined Al-Cu alloy in a rectangular sand mold. For the aluminum alloy studied, the equiaxed grains are lighter than the bulk melt and thus float up. Experiments were designed to investigate floatation phenomena of equiaxed grains in the presence of thermosolutal convection. Cooling curves were recorded at key locations in both the casting and the chill. Quantitative image analysis and spatial chemical analysis were performed on the solidified casting to observe the chemical and microstructural inhomogeneity created by the melt convection and solid floatation. Several notable features that can be attributed to grain movement were observed in temperature histories, macrosegregation patterns, and microstructures. In our experiments, the floatation of grains influences the thermal conditions and the overall flow direction in the casting cavity. In some cases, the induced flow resulting from the grain movement caused a flow reversal. This in turn influences the solidification direction, microstructure evolution, and the overall macrosegregation behavior.

Quantum phenomena in magnetic nano clusters

One of the fascinating fields of study in magnetism in recent years has been the study of quantum phenomena in nanosystems. While semiconductor structures have provided paradigms of nanosystems from the stand point of electronic phenomena the synthesis of high nuclearity transition metal complexes have provided examples of nano magnets. The range and diversity of the properties exhibited by these systems rivals its electronic counterparts. Qualitative understanding of these phenomena requires only a knowledge of basic physics, but quantitative study throws up many challenges that are similar to those encountered in the study of correlated electronic systems. In this article, a brief overview of the current trends in this area arc highlighted and some of the efforts of our group in developing a quantitative understanding of this field are outlined.

On cavity flow at high Reynolds numbers

The flow in a square cavity is studied by solving the full Navier–Stokes and energy equations numerically, employing finite-difference techniques. Solutions are obtained over a wide range of Reynolds numbers from 0 to 50000. The solutions show that only at very high Reynolds numbers (Re [gt-or-equal, slanted] 30000) does the flow in the cavity completely correspond to that assumed by Batchelor's model for separated flows. The flow and thermal fields at such high Reynolds numbers clearly exhibit a boundary-layer character. For the first time, it is demonstrated that the downstream secondary eddy grows and decays in a manner similar to the upstream one. The upstream and downstream secondary eddies remain completely viscous throughout the range of Reynolds numbers of their existence. It is suggested that the behaviour of the secondary eddies may be characteristic of internal separated flows.

The Effect of Evacuated Backside Cavity on the Dynamic Characteristics of a Capacitive Micromachined Ultrasonic Transducer

In this paper, we investigate the effect of vacuum sealing the backside cavity of a Capacitive Micromachined Ultrasonic Transducer (CMUT). The presence or absence of air inside the cavity has a marked effect upon the system parameters, such as the natural frequency, damping, and the pull-in voltage. The presence of vacuum inside the cavity of the device causes a reduction in the effective gap height which leads to a reduction in the pull-in voltage. We carry out ANSYS simulations to quantify this reduction. The presence of vacuum inside the cavity of the device causes stress stiffening of the membrane, which changes the natural frequency of the device. A prestressed modal analysis is carried out to determine the change in natural frequency due to stress stiffening. The equivalent circuit method is used to evaluate the performance of the device in the receiver mode. The lumped parameters of the device are obtained and an equivalent circuit model of the device is constructed to determine the open circuit receiving sensitivity of the device. The effect of air in the cavity is included by incorporating an equivalent compliance and an equivalent resistance in the equivalent circuit.

Analytical Evaluation of Squeeze Film Forces in a CMUT With Sealed Air-Filled Cavity

The presence of vacuum inside the cavity of a capacitive micromachined ultrasonic transducer (CMUT) causes the membrane of the device (which is the main vibrating structural component) to deflect towards the substrate, thereby causing a reduction in the effective gap height. This reduction causes a drastic decrease in the pull-in voltage of the device limiting the DC bias at which the device can be operated for maximum efficiency. In addition, this initial deflection of the membrane due to atmospheric pressure, causes significant stress stiffening of the the membrane, changing the natural frequency of the device significantly from the design value. To circumvent the deleterious effects of vacuum in the sealed cavity, we investigate the possibility of using sealed CMUT cavities with air inside at ambient pressure. In order to estimate the transducer loss due to the presence of air in the sealed cavity, we evaluate the resulting damping and determine the forces acting on the vibrating membrane resulting from the compression of the trapped air film. We take into account the flexure of the top vibrating membrane instead of assuming the motion to be parallel-plate like. Towards this end, we solve the linearized Reynolds equation using the appropriate boundary conditions and show that, for a sealed CMUT cavity, the presence of air does not cause any squeeze film damping.