Identifying dynamical bottlenecks of stochastic transitions in biochemical networks

In biochemical networks, identifying key proteins and protein-protein reactions that regulate fluctuation-driven transitions leading to pathological cellular function is an important challenge. Using large deviation theory, we develop a semianalytical method to determine how changes in protein expression and rate parameters of protein-protein reactions influence the rate of such transitions. Our formulas agree well with computationally costly direct simulations and are consistent with experiments. Our approach reveals qualitative features of key reactions that regulate stochastic transitions.     

Diversifying the structural architecture of synthetic oligomers: the hetero foldamer approach

Conformationally ordered synthetic oligomers, also called "foldamers", have attracted considerable attention in recent years owing to their ability to mimic the structural architecture of biopolymers and also because of their potential applications in biomedical and material science fields. Until recently, the major focus in this area has been the development of oligomers featuring a single type of monomer building blocks. However, due to the enormous possibility of augmenting the conformational space available for oligomer design, the hetero foldamer approach has been introduced very recently. This feature article aims to describe foldamers with unique structural architectures, exclusively featuring heterogeneous backbones (hetero foldamers).     

Poisson convergence of eigenvalues of circulant type matrices

We consider the point processes based on the eigenvalues of the reverse circulant, symmetric circulant and k-circulant matrices with i.i.d. entries and show that they converge to a Poisson random measures in vague topology. The joint convergence of upper ordered eigenvalues and their spacings follow from this. We extend these results partially to the situation where the entries are come from a two sided moving average process.     

Role of Plasma Parameters on the Conjugated Structure Retention in Polyaniline Thin Film

The role of plasma parameters on the film characteristics is investigated on polyaniline thin film deposited by radio frequency (RF) plasma polymerization. A series of un-doped and iodine doped polyaniline thin films are prepared by RF discharge operating at 13.56?MHz with different discharge powers and pressure variation from 0.1 to 0.05?mbar and variation in deposition time from 20 to 40?min. A good thin film is found with a power ranging from 9?W (?28?V self bias) to 20?W (?65?V self bias) at 0.1?mbar pressure which is confirmed by fourier transform infra-red spectroscopy showing the retention of aromatic rings. In addition, iodine doping is carried out with 9?W power and 0.1?mbar pressure. The characterization of process plasma is done using Langmuir probe diagnostics and optical emission spectroscopy. A correlation has been established between film characteristics and plasma properties investigated using optical emission spectroscopy and Langmuir probe analysis. Emphasis has been given on the study of the influence of plasma parameters, particularly of the electron energy distribution function on the quality of conjugated plasma polymerized aniline film.     

Mechanistic aspects of ligand substitution on [(H2O)(tap)2RuORu(tap)2(H2O)]2+ ion {tap = 2‐(m‐tolylazo)pyridine} by some amino acids in aqueous medium at physiological pH

The interaction of the title complex with selected amino acids such as glycine (L¹H), l ‐valine (L²H), and l ‐leucine (L³H) has been studied spectrophotometrically in aqueous medium as a function of [substrate complex], [ligand], and temperature. The reaction has been monitored at 600 nm, where the spectral difference between the reactant and product is maximum. At pH 7.4, the reaction has been found to proceed via two distinct consecutive steps, i.e., it shows a nonlinear dependence on the concentration of ligands: The first process is [ligand] dependent, but the second step is [ligand] independent. The rate constants for the processes are k₁～10^?3 s^?1 and k₂～10^?4 s ^?1. The activation parameters were calculated from Eyring plots. Based on the kinetic and activation parameters, an associative interchange mechanism is proposed for the interaction processes. From the temperature dependence of the outer sphere association equilibrium constant, the thermodynamic parameters were also calculated, which gives a negative Δ G^o value for both the steps at all temperatures studied, supporting the spontaneous formation of an outer sphere association complex. The product of the reaction has been characterized with the help of conductance measurement, IR, NMR, and ESI‐mass spectroscopic analysis. © 2012 Wiley Periodicals, Inc. Int J Chem Kinet 44: 612–623, 2012     

Limiting spectral distributions of some band matrices

We use the method of moments to establish the limiting spectral distribution (LSD) of appropriately scaled large dimensional random symmetric circulant, reverse circulant, Toeplitz and Hankel matrices which have suitable band structures. The input sequence used to construct these matrices is assumed to be either i.i.d. with mean zero and variance one or independent and appropriate finite fourth moment. The class of LSD includes the normal and the symmetrized square root of chi-square with two degrees of freedom. In several other cases, explicit forms of the limit do not seem to be obtainable but the limits can be shown to be symmetric and their second and the fourth moments can be calculated with some effort. Simulations suggest some further properties of the limits.     

Radiation effect on temperature distribution and NO formation in a diffusion flame under reduced gravity conditions

Combustion of hydrocarbon fuel is accompanied with the formation of nitric oxide (NO) amongst other harmful emissions. In this work, a numerical investigation has been made for understanding the effect of radiative heat transfer on temperature distribution and formation of thermal NO in a methane–air diffusion flame under different reduced gravity environments. Conservation equations of overall mass, species concentration, momentum and energy for the reactive flows have been numerically solved with the use of finite difference scheme. In addition to that a semi-empirical soot model and an optically thin radiation model have been incorporated in the simulation. Gravity level is varied by the changed values of acceleration due to gravity. A thermal NO model incorporated accounts for the NO formation process which is decoupled from the hydrocarbon combustion. The relevant conservation equations have been solved as a post combustion reaction process. The flame height drops marginally with the reduction of gravity. Temperature becomes more uniformly distributed at lower gravity. NO formation boosts up with the fall of gravity below normal level when no radiation effect is considered. However, when radiation is considered, NO formation declines marginally with the reduction of gravity levels. Also in this case, concentration values of NO compare substantially lower with those without radiation. The upsurge of NO formation due to decline in gravity; and on the other hand, a shrinkage in concentration values of NO due to radiation effect can be attributed mainly to the rise and fall of temperature respectively in the computational zone.     

Kinetics and mechanism of the interaction of adenosine with cis‐diaqua(cis‐1,2‐diaminocyclohexane)platinum(II) perchlorate in aqueous medium

The kinetics of the interaction of adenosine with cis‐[Pt(cis‐dach)(OH₂)₂]²⁺ (dach = diaminocyclohexane) was studied spectrophotometrically as a function of [cis‐[Pt(cis‐dach)(OH₂)₂]²⁺], [adenosine], and temperature at a particular pH (4.0), where the substrate complex exists predominantly as the diaqua species and the ligand adenosine exists as a neutral molecule. The substitution reaction shows two consecutive steps: the first is the ligand‐assisted anation followed by a chelation step. The activation parameters for both the steps have been evaluated using Eyring equation. The low negative value of ΔH^≠₁ (43.1 ± 1.3 kJ mol^?1) and the large negative value of ΔS^≠₁ (?177 ± 4 J K^?1 mol^?1) along with ΔH^≠₂ (47.9 ± 1.8 kJ mol^?1) and ΔS^≠₂ (?181 ± 6 J K^?1 mol^?1) indicate an associative mode of activation for both the aqua ligand substitution processes. The kinetic study was substantiated by infrared and electrospray ionization mass spectroscopic analysis. © 2011 Wiley Peiodicals, Inc. Int J Chem Kinet 43: 219–229, 2011     

Pd(0)-catalyzed intramolecular Heck reaction: A general route for fused oxepine derivatives

A simple and facile approach for the synthesis of various structurally different tricyclic bent oxepine frameworks from a readily accessible precursor has been introduced. The synthesis of substituted oxepine derivative involved Pd(0)-catalyzed Heck reaction. This methodology enriches the literature for the large ring formation.