Author
Nita Parekh
Other affiliations: Santa Fe Institute, National Chemical Laboratory, Jawaharlal Nehru University ...read more
Bio: Nita Parekh is an academic researcher from International Institute of Information Technology, Hyderabad. The author has contributed to research in topics: Coupled map lattice & Protein structure. The author has an hindex of 14, co-authored 45 publications receiving 650 citations. Previous affiliations of Nita Parekh include Santa Fe Institute & National Chemical Laboratory.
Papers
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TL;DR: A web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative analysis of residue–residue interactions in single chains, protein complex, modelled protein structures and trajectories and provides insights into structure-function relationship.
Abstract: Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue-residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in A) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein-protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/.
131 citations
TL;DR: In this article, a simple method, using constant pinnings, was proposed to suppress spatiotemporal chaos and achieve global control in coupled map lattice models under different situations, e.g., for uniform pinning, non-uniform pinning with regular or random distributions, and lattices with spatial heterogeneity in local dynamics and coupling strength.
Abstract: We present a simple method, using constant pinnings, to suppress spatiotemporal chaos and achieve global control in coupled map lattice models under different situations, e.g., for uniform pinning, nonuniform pinning with regular or random distributions, and lattices with spatial heterogeneity in local dynamics and coupling strength. The method is easy to implement and does not require any a priori information of the system dynamics or explicit changes in its parameters. This method can also be used for local control of spatiotemporal dynamics, an aspect that has crucial importance in many natural systems.
115 citations
TL;DR: In this article, the authors developed a novel numerical approach based on a computationally efficient cell dynamical system (CDS) model, for studying the kinetics of ordering in systems (described by a nonconserved order parameter) with quenched disorder, evolving from unstable initial states.
Abstract: The authors develop a novel numerical approach, based on a computationally efficient cell dynamical system (CDS) model, for studying the kinetics of ordering in systems (described by a non-conserved order parameter) with quenched disorder, evolving from unstable initial states. They use this model to study the kinetics of domain growth in a coarse-grained version of the random exchange Ising model. Their numerical data strongly indicate quantitative agreement with the theoretically predicted asymptotic growth law over a limited range of disorder amplitudes. They also compare their observations with those in laboratory experiments and make important predictions regarding dynamical scaling in these systems.
57 citations
TL;DR: The effect of sequencing coverage, read length, bin size, data pre-treatment and segmentation approaches on accurate detection of the complete spectrum of CNVs is shown.
Abstract: Discovery of copy number variations (CNVs), a major category of structural variations, have dramatically changed our understanding of differences between individuals and provide an alternate paradigm for the genetic basis of human diseases. CNVs include both copy gain and copy loss events and their detection genome-wide is now possible using high-throughput, low-cost next generation sequencing (NGS) methods. However, accurate detection of CNVs from NGS data is not straightforward due to non-uniform coverage of reads resulting from various systemic biases. We have developed an integrated platform, iCopyDAV, to handle some of these issues in CNV detection in whole genome NGS data. It has a modular framework comprising five major modules: data pre-treatment, segmentation, variant calling, annotation and visualization. An important feature of iCopyDAV is the functional annotation module that enables the user to identify and prioritize CNVs encompassing various functional elements, genomic features and disease-associations. Parallelization of the segmentation algorithms makes the iCopyDAV platform even accessible on a desktop. Here we show the effect of sequencing coverage, read length, bin size, data pre-treatment and segmentation approaches on accurate detection of the complete spectrum of CNVs. Performance of iCopyDAV is evaluated on both simulated data and real data for different sequencing depths. It is an open-source integrated pipeline available at https://github.com/vogetihrsh/icopydav and as Docker's image at http://bioinf.iiit.ac.in/icopydav/.
42 citations
TL;DR: NAPS as discussed by the authors is a method of choice to gain insights in understanding protein structure, folding and function, which is an invaluable tool with widespread applications such as analyzing subtle conformational changes and flexibility regions in proteins, dynamic correlation analysis across distant regions for allosteric communications, in drug design to reveal alternative binding pockets for drugs, etc.
Abstract: Network theory is now a method of choice to gain insights in understanding protein structure, folding and function. In combination with molecular dynamics (MD) simulations, it is an invaluable tool with widespread applications such as analyzing subtle conformational changes and flexibility regions in proteins, dynamic correlation analysis across distant regions for allosteric communications, in drug design to reveal alternative binding pockets for drugs, etc. Updated version of NAPS now facilitates network analysis of the complete repertoire of these biomolecules, i.e., proteins, protein-protein/nucleic acid complexes, MD trajectories, and RNA. Various options provided for analysis of MD trajectories include individual network construction and analysis of intermediate time-steps, comparative analysis of these networks, construction and analysis of average network of the ensemble of trajectories and dynamic cross-correlations. For protein-nucleic acid complexes, networks of the whole complex as well as that of the interface can be constructed and analyzed. For analysis of proteins, protein-protein complexes and MD trajectories, network construction based on inter-residue interaction energies with realistic edge-weights obtained from standard force fields is provided to capture the atomistic details. Updated version of NAPS also provides improved visualization features, interactive plots and bulk execution. URL: http://bioinf.iiit.ac.in/NAPS/.
40 citations
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01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.
4,833 citations
TL;DR: Synchronization of chaos refers to a process where two chaotic systems adjust a given property of their motion to a common behavior due to a coupling or to a forcing (periodical or noisy) as discussed by the authors.
2,266 citations
TL;DR: The theory of phase-ordering dynamics that is the growth of order through domain coarsening when a system is quenched from the homogeneous phase into a broken-symmetry phase, with the emphasis on recent developments, is reviewed in this paper.
Abstract: The theory of phase-ordering dynamics that is the growth of order through domain coarsening when a system is quenched from the homogeneous phase into a broken-symmetry phase, is reviewed, with the emphasis on recent developments. Interest will focus on the scaling regime that develops at long times after the quench. How can one determine the growth laws that describe the time dependence of characteristic length scales, and what can be said about the form of the associated scaling functions? Particular attention will be paid to systems described by more complicated order parameters than the simple scalars usually considered, for example vector and tensor fields. The latter are needed, for example, to describe phase ordering in nematic liquid crystals, on which there have been a number of recent experiments. The study of topological defects (domain walls, vortices, strings and monopoles) provides a unifying framework for discussing coarsening in these different systems.
2,130 citations
TL;DR: Surprisingly, it is found that a network under a typical framework can realize synchronization subject to any linear feedback pinning scheme by using adaptive tuning of the coupling strength.
962 citations
TL;DR: In this paper, a single controller can pin a coupled complex network to a homogeneous solution, and sufficient conditions are presented to guarantee the convergence of the pinning process locally and globally.
Abstract: In this paper, without assuming symmetry, irreducibility, or linearity of the couplings, we prove that a single controller can pin a coupled complex network to a homogenous solution. Sufficient conditions are presented to guarantee the convergence of the pinning process locally and globally. An effective approach to adapt the coupling strength is proposed. Several numerical simulations are given to verify our theoretical analysis.
945 citations