Structural Studies on Ni75(SnSi)25 and Ni75(SnBi)25 Alloys

Ternary alloys on the quasi-binary system Ni₃Sn(r) in equilibrium condition. It has been observed that these phases undergo transformations at high temperatures but upto 500 °C room temperature modifications are stable. The two phases do not have any appreciable solid solubility in either of them. The phase Ni₃Si(r) crystallizes in to Cu₃Au (Li₂) structure where as Ni₃Sn(r) is based on c.p.h. structure with a = 5.305 A°, c = 4.254 A°. No new ternary phase has been detected in Ni₃Sn Ni₃Si section. The investigated alloys of the Ni Sn Bi system contain 75 at.% Ni. All the ternary alloys show simultaneous occurrence of three phases, namely Ni₃Sn(r), NiBi and Ni(Sn) in equilibrium state. The phase NiBi has NiAs(B8) type of structure. Due to non-existence of isostructural phases in the two binary systems (Ni Sn and Ni Bi), single solid solution phases are not formed. Widely differing atomic sizes of nickel and bismuth atoms restrict the formation of solid solution of bismuth in nickel in contrast to Ni(Sn) where atomic size factor is favourable.     

Condensed history Monte Carlo methods for photon transport problems

We study methods for accelerating Monte Carlo simulations that retain most of the accuracy of conventional Monte Carlo algorithms. These methods - called Condensed History (CH) methods - have been very successfully used to model the transport of ionizing radiation in turbid systems. Our primary objective is to determine whether or not such methods might apply equally well to the transport of photons in biological tissue. In an attempt to unify the derivations, we invoke results obtained first by Lewis, Goudsmit and Saunderson and later improved by Larsen and Tolar. We outline how two of the most promising of the CH models - one based on satisfying certain similarity relations and the second making use of a scattering phase function that permits only discrete directional changes - can be developed using these approaches. The main idea is to exploit the connection between the space-angle moments of the radiance and the angular moments of the scattering phase function. We compare the results obtained when the two CH models studied are used to simulate an idealized tissue transport problem. The numerical results support our findings based on the theoretical derivations and suggest that CH models should play a useful role in modeling light-tissue interactions.     

PSPICE circuit simulation of microbolometer infrared detectors with noise sources

In this paper, we present a method of incorporating various types of noise in circuit simulation of a microbolometer infrared detector to analyze the effect of noise on its performance. This ability of simulating electro-thermal performance of microbolometers in circuit simulation platform along with their noise performance allows designing of its suitable readout integrated circuit (ROIC). Being an electro-thermal device, a microbolometer has both the electrical and thermal components interacting with each other. Therefore, the noise sources existing in standard circuit simulators cannot predict the noise of a microbolometer correctly. Disturbances coming from the background radiation, device temperature fluctuations, flicker noise and the Johnson noise etc. contribute in the total noise of a microbolometer element. All these components of noise can be incorporated using the proposed simulation technique. The technique also allows modifying the frequency response of the noise in simulations as per the user defined noise spectrum, making it suitable for any type of microbolometer.     

Preferential mode of cyclization of tetrahydrofuran amino acids containing peptides: some theoretical insights

Theoretical insights have been provided for the observed preference of cyclodimerization over intramolecular cyclization reactions in linear tripeptides containing “2,5‐cis” (2S,5R)‐tetrahydrofuran amino acid as well as in those containing “2,5‐trans” (2S,5S)‐tetrahydrofuran amino acid, using quantum chemical methods. The geometries of species involved as well as the feasibility of cyclization reactions are studied at the B3LYP/6‐31G(d,p) level of theory in gas phase as well as in solvent phase. Thermodynamic data from Hessian calculations favor the intermolecular cyclization. Analysis of optimized geometries reveals the existence of additional stabilizing hydrogen bonding interactions in intermolecularly cyclized products. The existence of these second‐order interactions is substantiated by topological (atoms in molecules (AIM)) and natural bond orbital (NBO) analyses. Such interactions are absent in the intramolecular cyclization products. Further justification for the presence of stabilizing interactions in intermolecularly cyclized products comes from the molecular electrostatic potentials and electron density surfaces. Kinetic control favoring the intermolecularly cyclized products due to additional entropy of activation in the intramolecular case is surmised. Copyright © 2009 John Wiley & Sons, Ltd.     

Front Cover: Can Cyanuric Acid and 2,4,6-Triaminopyrimidine Containing Ribonucleosides be Components of Prebiotic RNA? Insights from QM Calculations and MD Simulations (ChemPhysChem 11/2019)

As a step toward assessing their fitness as pre-RNA nucleobases, we employ DFT and MD simulations to analyze the noncovalent interactions of cyanuric acid (CA) and 2,4,6-triaminopyrimidine (TAP), and the structural properties of the associated ribonucleosides (rNs) and oligonucleotides. Our calculations reveal that the TAP : CA pair has a comparable hydrogen-bond strength to the canonical A : U pair. This strengthens the candidature of CA and TAP as prebiotic nucleobases. Further, the stacking between two canonical nucleobases is stronger than those between TAP or CA and a canonical base, as well as those between two TAP and/or CA, which indicates that enhanced stacking may have served as a driving force for the evolution from prebiotic to canonical nucleobases. Similarities in the DFT-derived anti/syn rotational barriers and MD-derived (anti) glycosidic conformation of the CA and TAP rNs and canonical rNs further substantiate their candidature as pre-RNA components. Greater deglycosylation barriers (as obtained by DFT calculations) for TAP rNs compared to canonical rNs suggest TAP rNs indicate higher resistance to environmental factors, while lower barriers indicate that CA rNs were likely more suitable for less-challenging locations. Finally, the tight packing in narrow CA:TAP-containing helices suggests that the prebiotic polymers were shielded from water, which would aid their evolution into self-replicating systems. Our calculations thus support proposals that CA and TAP can act as nucleobases of pre-RNA.     

Random walk on a self-avoiding walk with superconducting local bridges

Random walk on a self-avoiding walk with superconducting local bridges is studied by Real Space renormalization group technique. We enumerate SAWs in two dimensions for a square lattice by using corner rule and equal averaging method. For a SAW network with superconducting bridges we estimate the exponents for end to end resistance and linear part as 0.8625 and 0.81907 respectively. We also obtain the shortest path exponent =0.9782 by equal averaging technique.     

Static and dynamic models of biological networks

We consider static and dynamic approaches to the specification of probability distributions on graphs, consistent with desired statistical properties such as degree distributions, for use in modeling biological networks. In the static approach we develop analytical approximations to the Hamiltonian and partition functions. In the dynamic approach, we use a stochastic parameterized grammar to construct an evolutionary tree in which the nodes represent elements such as genes or cells and the links represent inheritance relations between the nodes. The grammar then constructs a network based on the feature vectors of the nodes in the tree. © 2006 Wiley Periodicals, Inc. Complexity 11:57–63, 2006     

Quantum control of vibrational excitations in a heteronuclear diatomic molecule

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 method^21,24 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.     

Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

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. 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.