http://192.168.1.40:8080/xmlui/handle/123456789/1112 2026-05-31T10:36:55Z http://192.168.1.40:8080/xmlui/handle/123456789/2326 Noise characteristics of feed forward loops Ghosh, Bhaswar; Karmakar, Rajesh; Bose, Indrani A prominent feature of gene transcription regulatory networks is the presence in large numbers of motifs, i.e., patterns of interconnection, in the networks. One such motif is the feed forward loop (FFL) consisting of three genes X, Y and Z. The protein product x of X controls the synthesis of protein product y of Y. Proteins x and y jointly regulate the synthesis of z proteins from the gene Z. The FFLs, depending on the nature of the regulating interactions, can be of eight different types which can again be classified into two categories: coherent and incoherent. In this paper, we study the noise characteristics of FFLs using the Langevin formalism and the Monte Carlo simulation technique based on the Gillespie algorithm. We calculate the variances around the mean protein levels in the steady states of the FFLs and find that, in the case of coherent FFLs, the most abundant FFL, namely, the type-1 coherent FFL, is the least noisy. This is shown to be true for all parameter values when the FFLs operate above their thresholds of activation/repression. In the case of incoherent FFLs, no such general conclusion can be shown. The results suggest possible relationships between noise, functionality and abundance. DOI: 10.1088/1478/3967/2/1/005 2005-03-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2325 Spin gap antiferromagnets: Materials and phenomena Bose, Indrani There are several interacting spin systems which have a gap in their spin excitation spectra. The gap does not occur due to anisotropies present in the system but is quantum mechanical in origin. We give a brief overview on different types of spin gap (SG) antiferromagnets, the models proposed to describe their physical properties and experimental realizations of such systems. Our special focus is on exactly-solvable models and rigorous theories which provide the correct physical picture for the novel phenomena exhibited by SG systems. 2005-01-10T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2323 Motifs in gene transcription regulatory networks Bose, Indrani; Ghosh, Bhaswar; Karmakar, Rajesh A brief overview is given of the structure and evolution of gene transcription regulatory networks (GTRNs) of simple organisms like Escherichia coli and yeast Saccharomyces cerevisiae. A prominent motif appearing in the GTRNs is the feed forward loop (FFL). The FFLs have essential functions in gene regulatory processes and it is desirable that the operational noise of a FFL be kept at the minimum for reliability of signal transmission. We calculate the variances around the mean protein levels in the steady states of Type-1 and Type-4 coherent FFLs using a stochastic model of gene expression and the Langevin formalism. The Type-1 FFL is found to be less noisy than the Type-4 FFL. Type-1 FFL motif is more abundant than Type-4 FFL motif in GTRNs. This leads to the conjecture that noise is one of the evolvable traits on which natural selection acts. DOI: 10.1016/j.physa.2004.08.049 2005-02-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2321 Graded and binary responses in stochastic gene expression Karmakar, Rajesh; Bose, Indrani Recently, several theoretical and experimental studies have been undertaken to probe the effect of stochasticity on gene expression (GE). In experiments, the GE response to an inducing signal in a cell, measured by the amount of mRNAs/proteins synthesized, is found to be either graded or binary. The latter type of response gives rise to a bimodal distribution in protein levels in an ensemble of cells. One possible origin of binary response is cellular bistability achieved through positive feedback or autoregulation. In this paper, we study a simple, stochastic model of GE and show that the origin of binary response lies exclusively in stochasticity. The transitions between the active and inactive states of the gene are random in nature. Graded and binary responses occur in the model depending on the relative stability of the activated and deactivated gene states with respect to that of mRNAs/proteins. The theoretical results on binary response provide a good description of the 'all-or-none' phenomenon observed in an eukaryotic system. DOI: 10.1088/1478-3967/1/4/001 2004-12-01T00:00:00Z