Name                                    : Dr. NITA PAREKH

Date of birth                         : 11-5-65

Marital status                      :  Married
                                                   Married name :  NITA TIWARI

Nationality                            :  Indian

Present address                      :  C/o Dr. Shrish Tiwari
(Home)                                         E503, BIC
                                                      Centre for Cellular and Molecular Biology
                                                      Uppal Road, Hyderabad - 500 007
                                                      Email : [email protected]
                                                      http://www.geocities.com/nitageo/

University academic               :  Ph.D. degree awarded in January 1995
record                                          Jawaharlal Nehru University, New Delhi, India.
                                                      Thesis Title : Pattern Formation in Spatially Extended Systems
                                                      Thesis Supervisor : Sanjay Puri

                                                      M.Phil. Degree in Physics, 1987 (1^st div.)
                                                      Rani Durgavati Vishwavidyalaya, Jabalpur.
                                                      Thesis Title : Vortex Line Solutions of theGinzburg-
                                                                    Landau theory of Superconductivity
                                                      Thesis Supervisor : Gautam Johri.

                                                      M.Sc. Degree in Physics, 1986 (1^st div.)
                                                      Rani Durgavati Vishwavidyalaya, Jabalpur.

                                                      B.Sc. Degree in Physics, Chemistry, Pure Mathematics, 1984 (1^st div.)
                                                      Rani Durgavati Vishwavidyalaya, Jabalpur

 Present position                    :  Assistant Professor
                                                    International Institute of Information Technology
                                                    Gachibowli
                                                    Hyderabad - 500 019
                                                    February 2003 - continuing

Research interests               :  Bioinformatics - DNA sequence analysis, Gene prediction
                                                    SNP and Haplotype analysis, proteomics
                                                    Characterization and control of Spatio-temporal systems
                                                    Phase Ordering Dynamics in binary alloys and polymers

Research experience          : 12yrs

Post-Doctoral experience:

1. Experimental modeling studies for multi-phase polymer processing,
    Center for Theoretical and Computational Materials Science, NIST, Maryland, U.S.A.
    June, 00 - May, 01

2. Theoretical studies of population growth under ecological processes,
    Centre for Cellular and Molecular Biology, Hyderabad
    July, 97 - May, 99

3. Design and analysis of chemical reactions/reactors with complex dynamics from scalar time-series data,
    Chemical Engineering Division, National Chemical Laboratory, Pune
    Aug., 94 - June, 97

Industrial Experience          :   1 ½ years in bioinformatics as Specialist - Genomics in the Ingenovis division of i-Labs Pvt. Ltd., Hyderabad.

Technical Skills:

Programming Languages  :  FORTRAN, C and BASIC

Operating Systems           :  UNIX, MS Windows, Mac OS, VMS

Software Used                  :  BLAST, Fasta, Tandem Repeat Finder, Combinatorial Extension
                                                Algorithm for structure superposition
                                                OOF, ABAQUS for mechanicanl properties analysis
                                                MATLAB, SIGMAPLOT

Modeling                          :  Dynamic Programming algorithms for sequence alignment,
                                             Combinatorial extension algorithms and Least-square minimization
                                             techniques for superposition of protein structures
                                             Statistical analysis in pattern search, identifying SNPs, etc.
                                             Partial differential equations, Monte Carlo (MC) simulations,
                                             Cell Dynamical System (CDS) modeling, Time-series data analysis
                                             Stress-Strain analysis of binary systems

Academic Distinctions:

1. Awarded CSIR Senior Research Associate (SRA) fellowship, September 2001.

2. UGC-CSIR NET cleared, 1997.

3. Best paper award at National Chemical Laboratory, Pune, 1996.

4. Awarded CSIR Research Associate (RA) fellowship, July 1994.

5. Selected speaker in Theoretical Physics Seminar Circuit (TPSC) programme, 1993.
6. Awarded CSIR Senior Research Fellowship (SRF), July 1991.

My major area of research has been the study of pattern forming systems - with a view to understand the occurrence and evolution of patterns and control/regulate them in the event of the system exhibiting undesirable behavior. Pattern formation is observed in a wide variety of physical, chemical, biological and engineering systems, and in the past few years I have focused on some of the important problems in this field. A brief description of my work is given below.

Computational Biology and Bioinformatics
 

Bioinformatics

Teaching experience: At present I am a faculty at the International Institute of Information Technology and teaching bioinformatics courses to B.Tech/B.C.A students. The courses taught so far include a course in biostatistics and biological databases and sequence analysis tools.

I have worked as a Genomics - Specialist at the bioinformatics division of i-Labs, ingenovis. This division was involved in producing products for the Bioinformatics community. My work involved forming a bridge between the research community and the industry - providing mathematical modeling expertise in the development of the software products, for DNA sequence analysis and proteomic. Some of the algorithms developed are for:

• Pair-wise Sequence Alignment: One of the important problems in bioinformatics is pair-wise alignment of DNA and protein sequences. The major problems with existing algorithms are that these are both memory and time extensive. We implemented dynamic programming algorithm based on Hirschberg?s space-optimal approach and distributed computing approach.
• Finding Tandem Repeats: Another important problem is finding repeat sequences in DNA. We developed an algorithm based on dynamic programming, but with conditions  incorporated such that simultaneous filling up of the matrix and traceback is possible, thus lifting the limitations on the sequence size, making whole genome analysis possible on a desktop. The distributed computing approach has been implemented for computational efficiency.
• Pair-wise Structural Alignment of Proteins: I was also involved in the development of an algorithm for structural alignment of proteins using combinatorial extension approach for optimal alignment and least-square minimization for superposition of homologous structures.
• Inferring Haplotypes from SNPs: Another project I initiated was aimed at developing an algorithm based on Clark?s parsimony approach for constructing haplotypes from a given set of single nucleotide polymorphisms (SNPs).
• Analysis of Mass Spectral data: I identified steps for implementing an algorithm for bacterial identification for SELDI-TOF-MS data. This involves comparison of the mass spectral data to identify and create a mass fingerprint database. It then involves implementing clustering algorithms on the significant peaks and output the result in the form of dendrograms.

Have worked with the Mathematical modeling group at the Center for Cellular and Molecular Biology (CCMB), Hyderabad. The work involved the modeling of ecological and excitable systems using Coupled map lattices (CMLs) and analyzing the behavior of the dynamics under different parametric situations. The focus of the study was to develop a method to suppress, enhance or induce chaos in spatiotemporal dynamical systems.

Coupled map lattices (CML) are being increasingly used in modeling biological systems as these offer computationally efficient models for the study of spatially extended nonlinear systems. Alterations in the normal functioning of these systems result may  their exhibiting undesired dynamical behavior, and thus the analysis and control of spatiotemporal dynamics have important implications in these systems. In a recent study we proposed a simple and novel method involving constant pinnings or perturbations in the spatial domain to regulate the system in a desired dynamical state. By pinning in this manner we actually affect (increase/decrease) the system variable, e.g., the population density of the interacting species in a chemically reacting system, changing voltage in an excitable tissue, etc. The major advantage of this method is that it does not require any a priori information of the system dynamics or its parameters for control. Also, the method can be used either for suppressing spatiotemporal chaos or for enhancing/inducing complex and chaotic oscillations in the dynamics.

Physical and Chemical Systems

Mechanical Properties of Polymers

The project involved the study of macroscopic properties of polymer blends, composites and glassy materials from an analysis of the microstructures - a challenging problem in materials science. It is well known that the performance and properties of devices made from these materials depend crucially on the microstructure that emerges during processing. And the present understanding of the non-equilibrium physics of morphogenesis in these materials is weak. Computer ``experiments'' allow fast, inexpensive and non-destructive prediction of materials properties and behavior. A finite-element code, "OOF" (developed by NIST scientists) was used for analyzing the microstructure and calculating macroscopic properties from micrographs of real materials. For studying the hyperelasticity of the polymer blends, the software tool ABAQUS was used. This was a joint-project of The Institute of Materials Science, University of Connecticut, Connecticut, and Center for Theoretical and Computational Materials Science, National Institute of Standards and Technology (NIST), Maryland, U.S.A.

Characterization and Control of Spatiotemporal Systems

A major part of this work was carried out at Chemical Engineering Division, National Chemical Laboratory (NCL), Pune.

In general the analysis of real experimental situations involve nonlinearity and spatial degrees of freedom. This has led to the study of spatially extended nonlinear systems. The known techniques for the characterization and control of low-dimensional systems are not easily extendable to spatio-temporal systems because of the large degrees of freedom. The need then arises for developing novel methods for the analysis of these high-dimensional systems. We carried out the characterization, synchronization and control of spatiotemporal patterns and spatiotemporal chaos with applications to chemical and biological systems, e.g., chemically reacting systems, coupled population dynamics, spatially extensive excitable media such as cardiac or neuronal tissues.

In a recent study we show that it is possible to characterize and control the full spatiotemporal dynamics in diffusively coupled model systems (both discrete and continuum) by an analysis in spatially localized regions, i.e., sub-systems. The study was carried out on a chemical reaction-diffusion model system with nonlinearity introduced via autocatalytic feedback steps. The major advantage of this method is that it enables considerable reduction in the computational effort, thus making the analysis of spatiotemporal systems practically feasible. The characterization and control method has also shown to work for coupled logistic and henon maps on spatially discrete lattices. Another important problem studied is the control of a special class of spatiotemporal patterns, e.g., spots, which replicate, grow and die as solutions of nonlinear chemical reaction-diffusion systems. The study of these patterns is interesting because of their striking resemblance to the phenomenon of self-replication observed in many important physical, chemical and biological systems, e.g., micelles and reverse micelles, morphogenesis of living cells, and DNA and RNA oligomers.

Phase Ordering Kinetics of Binary Systems

An important problem in non-equilibrium statistical physics is the kinetics of phase ordering which involves the temporal evolution of a homogeneous mixture of a two-phase system rendered thermodynamically unstable by a rapid quench below its critical temperature. The quenched system gradually evolves from the non-equilibrium homogeneous state towards an inhomogeneous thermal equilibrium state consisting of domains rich in the two distinct phases.  Our project involved systematically incorporating and studying the role of some experimentally relevant effects, such as, quenched disorders and anisotropic external fields in the dynamics of phase ordering systems. A novel numerical approach based on cell dynamical system (CDS) modeling was used to study the kinetics of domain growth in the presence of quenched disorder. Our results exhibited a slower logarithmic growth of the domains in the presence of disorder in conjunction with the experimental results. In the presence of external anisotropic fields, e.g., gravitational field varying linearly in one direction, we formulated a phenomenological model using mean field approximations. A faster, linear growth of the domains in the direction of the field was observed and the anisotropy was seen to break the dynamical scaling of the structure factor.

New Numerical Scheme for Fisher Equation

A new numerical scheme was proposed for solving nonlinear partial differential equations. We considered the Fisher equation for the study. Because of the nonlinearity, the discretised solution exhibits unstable ad chaotic oscillations, even when there is no chaos in the system. This problem is taken care of by first integrating the local nonlinear function (analytically or numerically) and then incorporating the diffusive process. We show that this new scheme is more stable than the conventional Euler and implicit numerical schemes even for very large space and time discretizations.

Velocity Selection in Coupled Map Lattices

We also studied velocity selection of travelling wavefronts in discretised Fisher equation and formulated a discrete analog of the "marginal stability hypothesis" to provide a theoretical basis of our results. A perturbative approach was carried out to understand this velocity selection.

1. A New Numerical Scheme for the Fisher Equation, Nita Parekh and S. Puri, J. Phys. A 23,    L1085
   (1990).

2. Non-algebraic Domain Growth in Random Magnets : A Cell Dynamical Approach, S. Puri, D.
    Chowdhury, and Nita Parekh, J. Phys. A 24, L1087 (1991).  [PDF]

3. Non-algebraic Domain Growth in Binary Alloys with Quenched Disorder, S. Puri and  Nita Parekh,
   J. Phys. A25, 4127 (1992).  [PDF]

4. Non-algebraic Domain Growth for Phase Ordering Dynamics in a Random Field, S. Puri and  Nita
     Parekh, J. Phys. A 26, 2777 (1993).  [PDF]

5. Velocity Selection in Coupled Map Lattices, Nita Parekh and S. Puri, Phys. Rev. E 47, 1415 (1993).  [PDF]

6. Phase Ordering Dynamics in a Gravitational Field, S. Puri, Nita Parekh and S. Dattagupta, J. Stat. Phys.
   75, 839 (1994).

7. Control of Self-Replicating Patterns in a Model Reaction-Diffusion System, Nita Parekh, V. Ravi
     Kumar and B.D. Kulkarni, Phys. Rev. E 52, 5100 (1995).  [PDF]

8. Analysis and Characterisation of Spatio-Temporal Patterns in Nonlinear Reaction-Diffusion
   systems, Nita Parekh, V. Ravi Kumar, and B.D. Kulkarni, Physica A 224, 369 (1996).  [PDF]

9. Control of Spatiotemporal Chaos : A Study with an Autocatalytic Reaction-Diffusion System,
     Nita Parekh, V. Ravi Kumar and B.D. Kulkarni, Pramana - J. Phys. 48, 303 (1997).

10. Synchronization and Control of Spatiotemporal Chaos Using Time-Series Data from Local
     Regions, Nita Parekh, V. Ravi Kumar and B.D. Kulkarni, Chaos 8, 300 (1998).  [PDF]

11. Global and Local Control of Spatiotemporal Chaos in Coupled Map Lattices, Nita Parekh, S.
       Parthasarthy  and S. Sinha, Phys. Rev. Lett. 81, 1401 (1998). [PDF]

12. Controlling Dynamics in Spatially Extended Systems, Nita Parekh and S. Sinha, Phys. Rev. E. 65,
      036227-1 to 9 (2002).  [PDF]

13. Controllability of Spatially Extended Systems Using the Pinning Approach, Nita Parekh and S. Sinha,
      to appear in Physica A.  [PDF]
 

In Conferences/Symposia :

1. Domain Growth in Disordered and Fractal Systems, Nita Parekh, B. Biswal, Puri and D. Chowdhury,
   Proceedings of the Solid State Physics Symposium, Vol. 35-C, (1992) DAE.

2. Phase Ordering Dynamics in Disordered Systems, Nita Parekh, S. Puri and D. Chowdhury in
   Computational  Aspects in Chaos and Nonlinear Dynamics, eds. G. Ambika and V.M. Nandakumaran [Wiley
   Eastern Limited, New  Delhi, 1994], pp. 263-273.

3. Presentation of the Ph.D. thesis titled "Pattern Formation in Spatially Extended Systems", Proceedings of
   the  Solid State Physics Symposium, Vol. 37, (1994) DAE.

4. Phase Ordering Dynamics in a Gravitational Field, S. Puri, Nita Parekh and S. Dattagupta, poster
    presentation at XIth International Congress of Mathematical Physics, Paris, France (July 1994).

5. Characterization and control of Spatiotemporal Chaos : Role of Sub-system Invariants, Nita Parekh,
    V. Ravi Kumar and B.D. Kulkarni, presented in:
(i) workshop on Recent Developments in Chaotic Dynamics at Centre for Nonlinear Dynamics, Bharatidasan
     University, Tiruchirapalli (1996);
(ii) International Conference on Dynamical Systems at Indian Institute of Science, Bangalore (January 1997).

6.  Suppression of Spatiotemporal Chaos in Coupled Map Lattices, Nita Parekh and S. Sinha in
     "Nonlinear Dynamicsand Brain Functioning", eds. N. Pradhan, P.E. Rapp and R. Sreenivasan [Nova Science
     Publishers, NY, 1999]

7. Suppression of Spatiotemporal Chaos in Coupled Map Lattices, Nita Parekh, S. Parthasarthy and S.
    Sinha, presented in International Conference on Nonlinear Dynamics: Integrability and Chaos, Centre for Nonlinear
    Dynamics Bharatidasan University, Tiruchirapalli (February 1998).

8. Controlling Spatiotemporal Chaos in Excitable Systems, Nita Parekh and S. Sinha, poster presentation at
    Fifth Experimental Chaos Conference, Orlando, Florida, USA (June 1999).

Referees :

1. Dr. Somdatta Sinha
    Scientist, Mathematical Modelling Group
    Centre for Cellular and Molecular Biology
    Uppal Road, Hyderabad - 500 007, INDIA.
    E-mail: [email protected]

2. Dr. C. Suguna
    Scientist, Mathematical Modelling Group
    Centre for Cellular and Molecular Biology
    Uppal Road, Hyderabad - 500 007, INDIA.
    E-mail: [email protected]

3. Dr. V. Ravi Kumar
    Scientist, Chemical Engineering Division
    National Chemical Laboratory
    Pune - 411 008, India
    E-mail: [email protected]

4. Dr. B. D. Kulkarni
    Head, Chemical Engineering Division
    National Chemical Laboratory
    Pune - 411 008, India
    E-mail: [email protected]

5. Dr. Martin Chiang
    Poly A205, Polymer Division
    Material Science and Engineering Laboratory
    National Institute of Standards and Technology (NIST)
    Gaithersberg, MD, 20899, U.S.A.
    Email:[email protected]