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Introduction
I am interested in various aspects of the origin and evolution of life and evolutionary dynamics in social complex systems. In the former domain, we are interested in understanding how the earliest RNA enzymes emerged via non-enzymatic processes and consequences of competition between protocells in a RNA world. In the latter domain, we use evolutionary game theory to understand the consequences of evolving individual choices on collective dynamics in scenarios of social conflict. We
Skills and Expertise
Additional affiliations
December 2011 - August 2022
Publications
Publications (132)
There have been two distinct phases of evolution of the genetic code: an ancient phase-prior to the divergence of the three domains of life, during which the standard genetic code was established-and a modern phase, in which many alternative codes have arisen in specific groups of genomes that differ only slightly from the standard code. Here we di...
Bribe demands present a social conflict scenario where decisions have wide-ranging economic and ethical consequences. Nevertheless, such incidents occur daily in many countries across the globe. Harassment bribery constitute a significant sub-set of such bribery incidents where a government official demands a bribe for providing a service to a citi...
Riboswitches are cis-regulatory non-coding genomic segments that control the expression of downstream genes by undergoing conformational change upon ligand binding. We present a comprehensive database of prokaryotic riboswitches that allows the user to search for riboswitches using multiple criteria, extract information about riboswitch location an...
The origin of a universal and optimal genetic code remains a compelling mystery in molecular biology and marks an essential step in the origin of DNA and protein based life. We examine a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences eac...
Harassment bribes, paid by citizens to corrupt officers for services the former are legally entitled to, constitute one of the most widespread forms of corruption in many countries. Nation states have adopted different policies to address this form of corruption. While some countries make both the bribe giver and the bribe taker equally liable for...
Humans navigate diverse social relationships and concurrently interact across multiple social contexts. An individual's behavior in one context can influence behavior in other contexts. Different payoffs associated with interactions in the different domains have motivated recent studies of the evolution of cooperation through the analysis of multic...
Strategies for sustaining cooperation and preventing exploitation by selfish agents in repeated games have mostly been restricted to Markovian strategies where the response of an agent depends on the actions in the previous round. Such strategies are characterized by lack of learning. However, learning from accumulated evidence over time and using...
The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Rece...
The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Rece...
The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA–lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting the system from being over-run by selfi...
The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA-lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favour the protocell promoting its growth and also protect the system from being over-run by paras...
We analyze a cooperative decision-making model that is based on individual aspiration levels using the framework of a public goods game in static and dynamic networks. Sensitivity to differences in payoff and dynamic aspiration levels modulates individual satisfaction and affects subsequent behavior. The collective outcome of such strategy changes...
The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of 'live', replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth...
We analyze a cooperative decision-making model that is based on individual aspiration levels using the framework of a public goods game in static and dynamic networks. Sensitivity to differences in payoff and dynamic aspiration levels modulate individual satisfaction and affects subsequent behavior. The collective outcome of such strategy changes d...
The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of 'live', replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth...
Societies rely on individual contributions to sustain public goods that benefit the entire community. Several mechanisms, that specify how individuals change their decisions based on past experiences, have been proposed to explain how altruists are not outcompeted by selfish counterparts. A key aspect of such strategy updates involves a comparison...
The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA enzymes from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined...
All societies rely on individual contributions to sustain public goods that benefit the entire community. A variety of mechanisms, that specify how individuals change their decisions in response to past experiences and behavioral attributes of interacting partners, have been proposed to explain how altruists are not outcompeted by selfish counterpa...
A bstract
The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA molecules with catalytic functions, from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA w...
We consider competition between antibiotic producing bacteria, non-producers (or cheaters), and sensitive cells in a two-dimensional lattice model. Previous work has shown that these three cell types can survive in spatial models due to the presence of spatial patterns, whereas coexistence is not possible in a well-mixed system. We extend this to c...
We consider competition between antibiotic producing bacteria, non-producers (or cheaters), and sensitive cells in a two-dimensional lattice model. Previous work has shown that these three cell types can survive in spatial models due to the presence of spatial patterns, whereas coexistence is not possible in a well-mixed system. We extend this to c...
Bribe demands present a social conflict scenario where decisions have wide-ranging economic and ethical consequences. Nevertheless, such incidents occur daily in many countries across the globe. Harassment bribery constitute a significant sub-set of such bribery incidents where a government official demands a bribe for providing a service to a citi...
Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 different classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi...
Riboswitches are cis-regulatory elements that regulate the expression of genes involved in biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of riboswitches discovered so far, three are known to regulate the concentration of biologically encoded amino acids glycine, lysine, and glutamine. While some comparative g...
Gross phylogenomic distribution of lysine riboswitches in Firmicutes.
The length of the red bars in the outer arc of the figure is correlated with the number of lysine riboswitches found in the corresponding species. This number is specified at the top of the bar.
(TIF)
Generalized model of operon formation and death and its relevance to regulation by lysine riboswitches.
(PDF)
SMART-BLAST results showing the strong similarity between the lysW gene of S. oneidensis and nhaC genes of other species that belong to the same clade.
(PDF)
Details of genomes where lysine riboswitches are present, the locations of the riboswitches in the genomic sequences and the corresponding gene/operon information.
(XLSX)
COGs used for the construction of the phylogenetic tree.
(XLSX)
We examine a scenario of social conflict that is manifest during an interaction between government servants providing a service and citizens who are legally entitled to the service, using evolutionary game-theory in structured populations characterized by an inter-dependent network. Bribe-demands by government servants during such transactions, cal...
Interspecific competition in bacteria governs colony growth dynamics and pattern formation. Here, we demonstrate an interesting phenomenon of interspecific competition between Bacillus cereus MSM-S1 and Pseudomonas sp. MSM-M1, where secretion of an inhibitor by Pseudomonas sp. is used as a strategy for survival. Although B. cereus grows faster than...
The phase explosion of water at a solid-water interface has been typically observed experimentally
with the use of pulsed lasers inducing cavitation bubbles near an absorbing surface. Here we show
that a tightly focused CW laser beam can be used to achieve phase explosion in a microscopic
domain inside a thin film of water in contact with a special...
Interspecific competition in bacteria governs colony growth dynamics and pattern formation. Here, we demonstrate an interesting phenomenon of interspecific competition between Bacillus cereus MSM-S1 and Pseudomonas sp. MSM-M1, where secretion of an inhibitor by Pseudomonas sp. is used as a strategy for the survival. Although B. cereus grows faster...
Interspecific competition in bacteria governs colony growth dynamics and pattern formation. Here, we demonstrate an interesting phenomenon of interspecific competition between Bacillus cereus MSM-S1 and Pseudomonas sp. MSM-M1, where secretion of an inhibitor by Pseudomonas sp. is used as a strategy for the survival. Although B. cereus grows faster...
Riboswitches are metabolite-sensing non-coding RNA located in the 5’ untranslated regions of bacteria and controlling gene expression of downstream genes. Their ability to specifically bind metabolites and catalyze reactions lends support to the RNA world hypothesis. Lysine-riboswitch is involved in de novo lysine synthesis in bacteria and contribu...
The phase explosion of water at a solid-water interface has been typically observed experimentally with the use of pulsed lasers inducing cavitation bubbles near an absorbing surface. Here we show that a tightly focused CW laser beam can be used to achieve phase explosion in a microscopic domain inside a thin film of water in contact with a special...
Summary: Riboswitches are non-coding RNA located in the 5' untranslated regions where they bind a target metabolite used to specify the riboswitch class and control the expression of associated genes. Accurate identification of riboswitches is the first step towards understanding their regulatory and functional roles in the cell. In this paper we d...
Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is to find additiona...
The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small numb...
The origin of the genetic code marked a major transition from a plausible RNA world to the world of DNA and proteins and is an important milestone in our understanding of the origin of life. We examine the efficacy of the physico-chemical hypothesis of code origin by carrying out simulations of code-sequence coevolution in finite populations in sta...
Riboswitches are regulatory RNA that control gene expression by undergoing conformational changes on ligand binding. Using phylogenetic analysis and comparative genomics we have been able to identify the class of genes/operons regulated by the purine riboswitch and obtain a high-resolution map of purine riboswitch distribution across all bacterial...
Supplementary file 1. Genes used for the construction of the phylogenetic tree of Firmicutes.
Supplementary file 2. Phylogenetic tree drawn using the NJ method with 1000 bootstrap replicates showing the points of origin of the various purine riboswitches in different shapes and colors.
Supplementary file 3. Phylogenetic tree drawn using the ML meth...
We have developed a 3D off-lattice stochastic polymerization model to study the subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips...
Accurate classification of HIV-1 subtypes is essential for studying the dynamic spatial distribution pattern of HIV-1 subtypes and also for developing effective methods of treatment that can be targeted to attack specific subtypes. We propose a classification method based on profile Hidden Markov Model that can accurately identify an unknown strain...
Subtype A classification using the improved method. (a) Distribution of Z-scores of group M sequences. (b) Frequency distribution of Z-scores when six sequences from subtype A are used to build the positive training set.
(PDF)
Classification of subtypes (a) H (b) J using the improved method. Three out of four sequences are used to construct the positive profile HMM for H and two out of four sequences are used to construct the positive profile HMM for J. In both cases, the remaining sequences are correctly classified.
(PDF)
Detection of subtype C in the gag-pol region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using sixteen sequences belonging to C. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Sub-subtype F1 classification using the improved method. (a) Distribution of Z-scores of group M sequences. (b) Frequency distribution of Z-scores when six sequences from subtype F1 are used to build the positive training set. The four sequences of subtype F2 have a Z-score close to zero indicating their close similarity to sequences of subtype F1....
Subtype G classification using the improved method. (a) Distribution of Z-scores of group M sequences. (b) Frequency distribution of Z-scores when six sequences from subtype G are used to build the positive training set.
(PDF)
Subtype D classification using the improved method when the env region is used to construct the positive and negative pHMMs. Distribution of Z-scores for group M sequences.
(TIF)
Subtype F1 classification using the improved method when the env region is used to construct the positive and negative pHMMs. Distribution of Z-scores for group M sequences.
(TIF)
Subtype H classification using the improved method when the env region is used to construct the positive and negative pHMMs. Distribution of Z-scores for group M sequences.
(TIF)
Detection of subtype A in the gag-pol region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e): all CRF strains when the positive training set is constructed using two sequences each belonging to A,A1 and A2. Abbreviations are used to label CRF strains in the X-axis. For example, the label 02 refers to CRF02_...
Detection of subtype G in the gag-pol region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using six sequences belonging to G. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Detection of subtype H in the gag-pol region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using four sequences belonging to H. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Subtype J classification using the improved method when the env region is used to construct the positive and negative pHMMs. Distribution of Z-scores for group M sequences.
(TIF)
Detection of subtype A in the env region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e): all CRF strains when the positive training set is constructed using a total of twelve sequences belonging to A,A1 and A2. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Detection of subtype J in the env region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using four sequences belonging to J. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Number of sequences making up the positive training set used for determining whether a given sub-type (X) is present in the
gag-pol
region of a CRF.
(PDF)
Subtype C classification using the improved method. (a) Distribution of Z-scores of group M sequences. (b) Frequency distribution of Z-scores when six sequences from subtype C are used to build the positive training set.
(PDF)
Detection of subtype D in the gag-pol region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using fourteen sequences belonging to D. The solid and dashed lines correspond to the thresholds Tp and Tn respectively. Subtype D is not detected only i...
Detection of subtype J in the gag-pol region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using three sequences belonging to J. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Subtype A classification using the improved method when the env region is used to construct the positive and negative pHMMs. Distribution of Z-scores for group M sequences.
(TIF)
Detection of subtype C in the env region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using ten sequences belonging to C. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Detection of subtype F in the env region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using twelve sequences belonging to F. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Accession numbers of sequences making up the positive training set for sub-type H and J when the gag-pol region is used for classification. Since there are only 4 sequences of the gag-pol region for H and 3 for J, 3 of the 4 sequences of H and 2 of the 3 sequences of J were used to build the respective pHMMs which were then successful in classifyin...
Accession numbers of sequences making up the negative training set for all sub-types except D when the
gag-pol
region is used for classification.
(PDF)
Accession numbers of sequences making up the negative training set for all sub-types, except H and J, when the
env
region is used for classification.
(PDF)
Accession numbers of sequences making up the negative training set for sub-type H when the
env
region is used for classification.
(PDF)
Accession numbers of sequences making up the negative training set for sub-type J when the
env
region is used for classification.
(PDF)
Subtype B classification using the improved method when the env region is used to construct the positive and negative pHMMs. Distribution of Z-scores for group M sequences.
(TIF)
Subtype C classification using the improved method when the env region is used to construct the positive and negative pHMMs. Distribution of Z-scores for group M sequences.
(TIF)
Subtype G classification using the improved method when the env region is used to construct the positive and negative pHMMs. Distribution of Z-scores for group M sequences.
(TIF)
Detection of subtype D in the env region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using twenty sequences belonging to D. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Accession numbers of sequences making up the positive training set for all sub-types except H & J when the
gag-pol
region is used for classification.
(PDF)
Accession numbers of sequences making up the negative training set for sub-type D when the
gag-pol
region is used for classification.
(PDF)
Accession numbers of sequences making up the positive training set for all sub-types, except H and J, when the
env
region is used for classification.
(PDF)
Number of sequences of each sub-type making up the negative training set used for determining whether a given sub-type (X) is present in the
env
region of a CRF.
(PDF)
Detection of subtype B in the env region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e): all CRF strains when the positive training set is constructed using thirty sequences each belonging to B. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Detection of subtype G in the env region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using twelve sequences belonging to G. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Detection of subtype H in the env region of CRF’s. The figures show the distribution of Z-scores of (a) pure sequences and (b)-(e) all CRF strains when the positive training set is constructed using four sequences belonging to H. The solid and dashed lines correspond to the thresholds Tp and Tn respectively.
(PDF)
Number of sequences of each sub-type making up the negative training set used for determining whether a given sub-type (X) is present in the
gag-pol
region of a CRF.
(PDF)
Thresholds for detection of sub-types in the
gag-pol
region of CRF strains.
(PDF)
Number of sequences making up the positive training set used for determining whether a given sub-type (X) is present in the
env
region of a CRF.
(PDF)
Thresholds for detection of sub-types in the
env
region of CRF strains.
(PDF)
Instructions for classifying a query sequence (Q) using our pHMM method.
(PDF)
Accession numbers of sequences making up the positive training set for sub-type H and J when the env region is used for classification. Since there are only 4 sequences of the env region for both H and J, three were used to build the pHMM which was then successful in classifying the remaining sequence. Note that a choice of any 3 of the 4 env seque...
We present a computational model of the E. coli Min oscillation that involves polymerization of MinD filaments followed by depolymerization stimulated by filament-end zones of MinE. Our stochastic model is fully three-dimensional, and tracks the diffusion and interactions of every MinD and MinE molecule. We recover self-organized Min oscillations....
ROC curve for Glms riboswitch family. PDF displaying ROC curve for Glms riboswitch family.
ROC curve for Purine riboswitch family. PDF displaying ROC curve for Purine riboswitch family.
ROC curve for Sam riboswitch family. PDF displaying ROC curve for Purine riboswitch family.
profile Hidden Markov Model for Sam riboswitch family. Text file displaying profile Hidden Markov Model for Sam riboswitch family.