Department of Chemical Engineering, IIT Bombay TAP and FA Ph.

D Topics for Autumn 2014
No. Faculty Name Project Details: PhD Positions for May 2014
1 Rochish
Thaokar
Numerical simulation of charged electrosprays for nanoparticle synthesis: Electrohydrodynamic atomization has
emerged as a powerful tool to produce nano-sized aerosols which are used in applications such as drug delivery, aerosol
generation for fundamental studies, nanoparticle synthesis, etc. The quantitative foundation of EHD systems is still
largely based on empirical scaling laws and there is considerable gap in providing predictive models for the particle size
and charge distribution craracterisitcs. More specifically, the challenge is to understand the mechanism of formation of
nano-sized particles from micron sized liquid droplets. The project aims as theoretical estimation (using analytical theory
and in-house BEM simulations as well as BEM based commercial softwares such as the Integrated Engineering Software)
of drop size after single and multiple Rayleigh fission of a charged drop and mechanisms to predict nano-sized droplets
produced in electrospray processes as well as predict droplet trajectories in a Electro-spray chamber. Who should apply:
Physics, Mechanical or Chemical Engineering, with inclination towards numerical simulations of fluids and electrostatics.
The candidate is expected to be versatile in numerical methods and fluid dynamics. (1 position, TAP/FA)
2 Rochish
Thaokar
Experimental investigation of electrospray systems: Electrohydrodynamic atomization has emerged as a powerful tool
to produce nano-sized aerosols which are used in applications such as drug delivery, aerosol generation for fundamental
studies, nanoparticle synthesis, etc. One of the challenges in the process is to understand the breakup of a single drop,
and its dependence on system parameters. The project would involve fabricating an experimental setup for investigation
of Rayleigh instability of a single charged drop, and its dependence on properties such as conductivity of the drop,
humidity and non-Newtonian and Viscoelastic character of the drop phase. Specifically, the setup will involve designing
and fabricating quadrupole field electrodes for stabilizing the drops, particle injection system etc. Who should apply:
Physics, Mechanical or Chemical Engineering, with inclination towards numerical simulations of fluids and electrostatics.
(1 position, TAP/FA)
3 Rochish
Thaokar and
Sameer Jadhav
(coguide)
Electroporation of liposomes decorated with nanoparticles and membrane modulating molecules for drug delivery:
Electroporation has emerged as a very effective way of gene and drug delivery. One of the challenges in electroporation is
to reduce the applied voltage (currently few kV DC pulses). Another important
technological issue is to have penetration of electric field inside a cell/vesicle. This experimental project aims at
understanding the interaction of electric field with lipid bilayers decorated with high dielectric constant nanoparticles
and membrane modulating molecules. The idea is to increase the effectiveness of electroporation by externally inducing
an increase in the effective electric permittivity of the bilayer. The project would involve video and fluorescence
microscopy of liposomes, decorated with nanoparticles and membrane modulating molecules subjected to various kinds
of electric signals. Who should apply: Students with Bio-Technology background with fellowships, should preferably have
experimental skills in microscopy, lipids, membranes (1 position, FA only)
4 Rochish
Thaokar and
Sameer Jadhav
(coguide)
Electrofusion of liposomes for drug delivery and nanoparticle synthesis: Liposomes based drug delivery, especially
for cancer treatment has gained significance in recent times due to their bio-compatibility and controlled release. A
controlled way of delivery is through application of electric field to induce electrofusion of the liposomes with cell
membrane. Another area where electrofusion is employed is the synthesis of niche chemicals and bio-compatible
nanoparticles. It is known that synthesis in confined environment helps in reducing the volume handled, contamination
etc. This experimental project aims at understanding the factors that control the electrofusion of liposomes with cells
or GUVs, with specific attention to the drug delivery aspects. It would also aim at controlled synthesis of biocompatible
nanoparticles using electrofusion. The project would involve video and fluorescence microscopy of liposomes and
microfluidics Who should apply: Students with Bio-Technology background with fellowships, should preferably have
experimental skills in microscopy, lipids, membranes (1 position, FA only)
5 Supreet Saini Community decisions in bacteria: This project deals with analysis of pathways which enable the single-cell organisms
(bacteria) to communicate with each other and take community decisions. This process is called Quorum sensing, and
is dictated by a regulatory networks inside the cell. In addition, many bacterial species have more than one system
for quorum sensing which enables them to (a) integrate multiple signals combinatorially, (b) keep track of rival specie
population, and (c) gauge local and distal population estimates. Development of an analytical and computational
framework to understand how these information is processed is the focus of this research. The work will involve
analysis and simulations in Matlab. This work is in collaboration with Dr. Sandeep Krishna at NCBS, Bangalore (http:/
/www.ncbs.res.in/sandeep). Relevant background: Courses in Differential Equations, Linear Algebra, Introductory
Probability & Statistics, and a strong interest in biology [Bachelors/Masters in Mathematics, Physics, Biotechnology,
Bioinformatics, Biochemical Engineering, Chemical Engineering, and other related fields.] (1 position, TAP/FA)
6 Supreet Saini Optimality of the Genetic Code: The genetic code can be thought of as an allocation problem where you have to allocate
64 codons among 21 boxes (one box for each amino acid, and another for translation stop sites) making sure that each
box gets at least one codon. With more than 10
80
ways to solve this counting problem, why is it that nature has chosen
the standard genetic code for this purpose? This project aims to explore the optimality, if any, of the standard genetic
code compared to other possible codes. The work will involve analysis and simulations in Perl. Relevant background:
Courses in Differential Equations, Linear Algebra, Introductory Probability & Statistics, and a strong interest in biology
[Bachelors/Masters in Mathematics, Physics, Biotechnology, Bioinformatics, Biochemical Engineering, Chemical
Engineering, and other related fields.] (1 position, TAP/FA)
7 K. V.
Venkatesh
Connecting genetic network response to metabolic network to characterize phenotypic response: The project deals
with characterizing the genetic network of E. coli for growth on various substrates and links the steady state response to
the metabolic network to quantify the phenotypic response. The project deals with experiments and theoretical analysis
of the system level behavior of growth of E. coli on various substrates both under aerobic and anaerobic conditions. The
project will also deal with characterizing metabolism of E. coli under nutritional shifts and under changing environmental
conditions such as temperature and pH. The project involves both wet lab and modeling genetic and metabolic networks.
The issue of optimal phenotypic shift under different conditions will be characterized. Who should apply: Students with
Biotechnology background and chemical engineering students with interest in Biochemical engineering are best suited. (1
position, FA only)
8 K. V.
Venkatesh
Analyzing whole body metabolism in Humans for characterizing disease states: Whole body metabolism in various
tissues is tightly regulated through several signaling networks. The project deals with analyzing the interconnections
between the signaling pathway and the metabolism. Structural and parametric perturbations for various lifestyle
conditions such as diet, exercise, infection will be studies to link the cause and effect for various lifestyle related diseases.
It is a theoretical project. Who should apply: Students with modeling experience are well suited, chemical engineering
background with interest in Biology and Biotechnology students are suited. (1 position, FA only)
9 Santosh
Noronha
Production of chiral drugs in modified microbial systems: The objective of this project is to overproduce a key chiral
pharma intermediate, currently extracted from plants. The strategies we propose to use include transferring pathways
to microbial systems from plants and other microbial systems, manipulation of pathway fluxes in these systems, and
engineering relevant enzymes to have improved catalytic activities. This is a collaborative project between IITB and a
regional ICMR lab. Who should apply: Candidates with M.Sc., or M.Tech Biochemistry or Biotechnology or equivalent.
Project-related experience with biochemistry, microbiology and molecular biology techniques would be an advantage.
Chemical engineering background candidates with project experience related to microbial biotechnology will also be
considered. (1 position, TAP/FA)
10 Santosh
Noronha
Real-time surgical evaluation of tumors using Raman spectroscopy. Brain tumors account for 85% to 90% of all primary
central nervous system (CNS) tumors. Brain tumors may be primary or secondary tumors. The primary tumors are named
based on the cell type from which they originate - astrocytoma arising from glial cells, meningioma from meninges and
oligodendroglioma arising from protective covering of the brain and are collectively referred to as gliomas. Gliomas
represent 30% of all brain tumors and 80% of all malignant tumors. These tumors are notoriously infiltrative and result in
poor prognosis; an important reason for this is the inability to adequately determine the position and extent of spread for
these tumor cells – an important determinant for outcome of a radical resection. Visual cues are often inadequate
primarily because the microscope is unable to visualize beyond the exposed surface. Deeper infiltrating tumor cells may
not be evident as the exposed surface of the resection cavity may appear “normal”. To enhance visualization, various
techniques of intraoperative imaging are employed; these require costly equipment to implement. Artifacts in the region
of the tumor cavity significantly limit interpretation of the images. Further, these modalities are not truly real-time but
necessitate interruption of the surgical procedure for acquiring images. The more recently introduced fluorescence guided
resection approach requires the administration of an external agent (aminolevulinic acid) to induce differential tissue
fluorescence which can then be visualized. A surgical microscope needs to be suitably modified for detecting
fluorescence. There is therefore a need for a rapid, objective technique conducive to real-time application that requires
little or no sample preparation. Raman spectroscopy is such a technique and can be adapted for real time, in vivo
applications. In recent work, the classification of normal and cancerous brain tissues has been reported using Raman
microspectroscopic and resonance Raman studies; necrotic tissue has also been differentiated from vital tumors. The
ability of fiber-optic Raman spectroscopy to distinguish normal brain samples from gliomas has recently been evaluated in
the Indian population, in a limited pilot study. These studies have been carried out at the Tata Memorial Center. The
proposed project is a collaborative study with TMC where we further develop these ideas by building in house Raman
spectroscopes, test these on animal tissues, and subsequently develop real time surgical margin evaluations in animal
models. Who should apply: Candidates with M.Tech. or B.Tech. in an engineering discipline with project-related
experience with electronics and hardware (preferably involving optics and spectroscopy). (1 position, TAP/FA)
11 Sameer
Jadhav,
Rochish
Thaokar
(coguide)
Molecular dynamics studies of phospholipid bilayers: Molecular dynamics has evolved into a critical tool for drug
discovery, design and screening. With more than sixty percent molecular targets for diseases being associated with
membranes, a better understanding of the phospholipid membrane interactions with relevant proteins and their ligands
is warranted. The objective of the work is to carry out molecular dynamics simulations using GROMACS to understand
how the biological membrane properties are modulated by various small molecules including siRNA and peptides. The
joint project in collaboration with ICT, Mumbai and NIRRH, Mumbai is funded by Nanomission, Department of Science
and Technology. Who should apply: Masters or Bachelor’s degree in Biotechnology, Chemical Engineering, Mechanical
Engineering or Master’s degree in Physics . Some computer programming experience is desirable. (1 position, TAP/FA)
12 Sameer
Jadhav,
Ganesh
Viswanathan
Modeling and simulation of molecular signaling during cell polarization: Division, orientation and migration of cells
require their polarization. We wish to simulate cellular response to chemical and mechanical signals by kinetic modeling
of the relevant molecular mechanisms. Of particular interest is signal attenuation/amplification due to interactions
between various pathways involved in cell polarization. The project will require extensive coding in C language / MATLAB.
(coguide) Who should apply: Masters or Bachelor’s degree in Biotechnology, Chemical Engineering, Mechanical Engineering or
Master’s degree in Physics. Some computer programming experience is desirable (1 position, TAP/FA)
13 Sameer Jadhav Development of liposomal systems for targeted delivery and controlled release of siRNA The siRNA based therapeutic
interventions have generated much interested in the treatment of genetic disorders. The objective of the project is to
develop liposome-based siRNA delivery systems and test their efficacy in vitro and in vivo. These small molecules are
known to alter the mechanical properties of biological membranes as well as modulate membrane interactions with
other surfaces. We plan to use micropipette aspiration which has been used to study biomembrane properties such as
area compressibility modulus, bending modulus, bilayer permeability and membrane lysis tension. The joint project in
collaboration with ICT, Mumbai and NIRRH, Mumbai is funded by Nanomission, Department of Science and Technology.
Who should apply: Masters or Bachelor’s degree in Biotechnology, Chemical Engineering, or Master’s degree in Pharmacy
(1 position, TAP/FA)
14 Mukta TripathyMiscibility and percolation in polymer - carbon nanotube composites Polymer-nanoparticle mixtures have a wide variety
of applications in industry due to their improved thermal, mechanical, rheological, electrical, and catalytic properties
over pure polymer melts. They are used to make better structural materials, as well as for several emerging high-
end utilities such as solar cells, fuel cells, biosensors, and tissue engineering. In particular, polymer-carbon nanotube
composites display remarkable improvements in strength and conductivity with only a small amout of nanotube present
in the mixture. To get these property improvements, the carbon nanotubes have to be both miscible in , and percolating
through the polymer matrix. However, solubilising carbon nanotubes in polymer has been a major challenge. This
study will determine the thermodynamic miscibility and percolation co-conditions for polymer-nanotube composites.
Theory and molecular simulations will be used for the study. Who should apply: Strong programming skills are a key
requirement. In addition the candidate should have the requisite background in linear algebra, differential equations, and
statistics. An introductory level understanding of statistical mechanics is preferred. Candidates with Physics / Physical
Chemistry / Chemical Engineering backgrounds are encouraged to apply. (1 position, TAP/FA)
15 Mukta TripathyThermodynamic Stability of Pickering Emulsions: Pickering emulsions are oil-in-water emulsions stabilized by
colloidal particles (rather than surfactant molecules) at the interface. The formation of these emulsions is usually not
spontaneous, indicating that they are not thermodynamically stable. They often require mechanical energy to be applied
(through stirring, jetting, etc.) to make them temporally stable. However, recent experiments report the spontaneous
formation of Pickering emulsions (*J. Phys. Chem. B* *114*, 12257 (2010)). It is clear that thermodynamic stability is
rather rare for these particle-stabilized emulsions. The object of our study is to theoretically determine the stability
conditions for Pickering emulsions. Who should apply: Strong programming skills are a key requirement. In addition the
candidate should have the requisite background in linear algebra, differential equations, and statistics. An introductory
level understanding of statistical mechanics is preferred. Candidates with Physics / Physical Chemistry / Chemical
Engineering backgrounds are encouraged to apply. (1 position, TAP/FA)
16 Mukta TripathyThe role of surface roughness in colloidal fluid structure: Colloidal particle systems are ubiquitous in manufacturing
products, biological systems, and nature in general. While most studies model colloidal particles as smooth hard spheres,
they do have surface roughness. The aim of this project is to determine the effect of roughness on colloidal fluid
structure, as well as its propensity to form condensed phases. Who should apply: Strong programming skills are a key
requirement. In addition the candidate should have the requisite background in linear algebra, differential equations, and
statistics. An introductory level understanding of statistical mechanics is preferred. Candidates with Physics / Physical
Chemistry / Chemical Engineering backgrounds are encouraged to apply. (1 position, TAP/FA)
17 Mukta TripathyPhase behavior of penetrable particles: Course-grained models of matter often involve representing matter as
larger penetrable spheres, rather than connected hard spheres. This project involves understanding the structure
and properties of these penetrable sphere systems, as a function of their density, penetrability, and stiffness. Initial
calculations have revealed very interesting clustering behavior. The aim of this project is to build on a few initial
calculations, to map-out a complete phase diagram for penetrable particle systems. The study will use statistical
mechanical tools and would involve computer programming. Who should apply: Strong programming skills are a key
requirement. In addition the candidate should have the requisite background in linear algebra, differential equations, and
statistics. An introductory level understanding of statistical mechanics is preferred. Candidates with Physics / Physical
Chemistry / Chemical Engineering backgrounds are encouraged to apply. (1 position, TAP/FA)
18 Abhijit
Majumder
To study the Combinatorial Effect of Bio-Chemical and Mechanical gradient on Cell Migration and Differentiation: A
micro-fluidic approach: Research in recent years has established that both chemical and mechanical signals are crucial in
determining almost every aspect of cell fate: cell division, maintenance, differentiation, quiescence and disease. Often,
the gradient of a signal plays a more critical role than the absolute concentration of that particular signal. This proposal
aims to explore the combinatorial effect of chemical and mechanical gradient on cell migration and differentiation by
developing a novel micro-fluidic based device. At present, availability of experimental assays to study simultaneous
gradients/attractants is poor. Even to study single chemical gradient, the choice of a device is limited and each device
comes with its own constraints such as additional shear stress on cells for flow-based devices or instability of the gradient
for static devices. In this proposal, I aim to design a micro-fluidic device which would be able to create a shear-free,
stable and robust chemical gradient. In addition, the device would be compatible with a substrate of gradient stiffness.
The chemical and mechanical gradient can be arranged in synch or at any other angle to study the effect of geometry.
The device will be initially tested with cell lines for their short-term and long-term migration. After the functionality of
the device is established, I envision using it to study the effect of chemical and mechanical gradient on differentiation of
embryonic and mesenchymal stem cells and migration of malignant cells to address questions related to regeneration
and metastasis. In particular, I would like to ask how multiple gradients influence patterning in a cell mass. Who should
apply: 1. Experience of cell culture, stem cell preferred. 2. Experience of molecular biology techniques 3. Interest in inter-
disciplinary research and drive to learn new techniques. (1 position, TAP/FA)
19 Jyoti Seth Flow and Rheology of Suspensions of Aggregated Lipids: Lipids often serve as structurants in foods, cosmetics,
pharmaceutics and biological materials. They form a network of aggregated nano-crystals that controls material rheology
and its functional efficacy. For example, flow behavior of fat-rich foods under confined shear affects their perceived
quality and taste. In this project, suspensions of model lipids will be studied under varying composition and growth
conditions. Experiments are being designed with the aim to decouple affects of nano-crystal growth and aggregation
on resultant microstructure, which will be correlated with material rheology. Interested students are encouraged
to refer the following paper. The PI may be contacted at jyoti@che.iitb.ac.in for any clarifications: Marangoni, A. G.,
Acevedo, N., Maleky, F., Co, E., Peyronel, F., Mazzanti, G., … Pink, D. (2012). Structure and functionality of edible fats.
Soft Matter, 8(5), 1275–1300. Who should apply: Chemical Engineering, Physics, Chemistry or Material Science. The
student will gain working knowledge of analytical techniques for characterization of microstructure and rheology of
suspensions. Understanding of transport phenomena, colloids is desired along with good communication skills. (1
position, TAP/FA)
20 Jyoti Seth Dynamic Simulations of Colloidal Glasses: Dense suspensions of particles are commonly present in cosmetic and
pharmaceutical products, biological systems, ceramics, etc. These materials have interesting flow properties and find
use as rheology modifiers, suspension stabilizers and drug delivery agents. In this project, simulations will be setup
to predict flow and rheological behavior of suspensions of soft particles as a function of the particle-particle and
particle-surface interactions. Interested students may read further in the following papers. The PI may be contacted at
jyoti@che.iitb.ac.in for clarifications. (1) Seth, J. R., Locatelli-Champagne, C., Monti, F., Bonnecaze, R. T., & Cloitre, M.
(2012). How do soft particle glasses yield and flow near solid surfaces? Soft Matter, 8(1), 140. doi:10.1039/c1sm06074k
(2) Seth, J. R., Mohan, L., Locatelli-Champagne, C., Cloitre, M., & Bonnecaze, R. T. (2011). A micromechanical model to
predict the flow of soft particle glasses. Nature Materials, 10(11), 838–43. doi:10.1038/nmat3119. Who should apply:
Chemical Engineering, Physics, Material Science or Mechanical Engineering. The project requires prior experience
with coding using least one of the programming languages - C, C++, Fortran, MATLAB. Past experience with modeling,
simulation or experimental experience with complex fluids will be a plus. The student will get an opportunity to learn and
apply simulation techniques such as Molecular Dynamics and Brownian Dynamics. (1 position, TAP/FA)
21 Jyoti Seth Fatty acid-Soap Complexes: Phase Behavior and Rheology: Fatty Acids (R-COOH) form molecular complexes with
corresponding soaps (viz., R-COONa), which serve as key ingredients in cleaning products (soaps, facial cleaners, shaving
creams), topical-delivery agents, etc. Stoichiometric complexes of fatty acid and soap result from hydrogen bonds formed
between carboxyl and carbonyl groups of the two molecules. These materials are also of fundamental interest as they
exhibit thermotropic phase transitions, which are often accompanied by abrupt change in bulk behavior. For example,
the material may switch from behaving like a free flowing fluid to a solid-like material due to heating or cooling across a
phase boundary. This project is being planned with an industrial partner and will explore fundamental aspects of acid-
soap complexes when modified with surfactants. Interested students may read further in the following papers. The PI
may be contacted at jyoti@che.iitb.ac.in for clarifications. (1) Cistola, D. P., Atkinson, D., Hamilton, J. A., & Small, D. M.,
(1986). Phase behavior and Bilayer Properties of Fatty Acids: Hydrated 1:1 Acid-Soaps, Biochemistry, 25 2804-2812. (2)
Pudney, P. D. A., Mutch, K. J., & Zhu, S. (2009). Characterising the phase behavior of stearic acid and its triethanolamine
soap and acid-soap by infrared spectrscopy. Physical Chemistry Chemical Physics, 11, 5010–5018. doi:10.1039/b819582j
Who should apply: Chemical Engineering, Physics, Chemistry or Material Science. The project is experimental in nature
and a hands-on approach is desired. The student will gain working knowledge of several analytical techniques for
characterization of microstructure and rheological behavior. Understanding of phase behavior and colloidal suspensions
is desired and good communication skills will be a plus. (1 position, TAP/FA)
22 Jyoti Seth Multi-scale Simulations for Understanding Rheological Behavior of Lipid Suspensions:
Multi-scale simulations have been planned to understand crystal growth and aggregation processes occurring during
preparation of suspensions of lipids. Lipids often serve as structurants in foods, cosmetics, pharmaceutics and biological
materials. They form a network of aggregated nano-crystals that controls material rheology and its functional efficacy.
For example, flow behavior of fat-rich foods under confined shear affects their perceived quality and taste. The aim is to
understand kinetics of nano-crystal growth and aggregation processes that occur over different length and time scales.
It is therefore challenging to combine both contributions and predict the microstructure of the material. Our aim is to
correlate the process of preparation with the microstructure so that material rheology may be controlled. Predictions
from simulations will be compared and verified against experimental measurements.Interested students may read further
in the following papers. The PI may be contacted at jyoti@che.iitb.ac.in for clarifications. (1) Anwar, J., & Zahn, D. (2011).
Uncovering molecular processes in crystal nucleation and growth by using molecular simulation. Angewandte Chemie -
International Edition, 50(9), 1996–2013. (2) Marangoni, A. G., Acevedo, N., Maleky, F., Co, E., Peyronel, F., Mazzanti, G.,
… Pink, D. (2012). Structure and functionality of edible fats. Soft Matter, 8(5), 1275–1300. Who should apply: Chemical
Engineering, Physics, Chemistry or Material Science. Ability to write and modify programs in C, C++ or Fortran is a must.
Past experience with modeling and simulation and experimental experience with complex fluids will be a plus. The
student will get the opportunity to develop and contribute routines for techniques such as Molecular Dynamics and
Monte Carlo simulations. Overall the student will learn about complex fluids, particularly about suspensions that are of
interest to many industries. (1 position, TAP/FA)
23 Ganesh
Viswanathan
Inter-linked feedback loop dynamics during Tumor Necrosis Factor alpha signaling in mammalian systems: Interlinked
feedback loops (IFL) are ubiquitously found in mammalian cytokine signaling networks and are emerging as novel
structures that dictate the cellular decision making process. The goal of this project is to construct single-cell and
population level predictive mathematical models of an IFL that is activated during TNF alpha cytokine signaling. The model
developed will be constrained by the experimental data generated in-house. This project will involve use of bifurcation
tools and probability theory. Numerical simulations will be conducted on high-performance computing facility. Codes
will be written in Matlab and/or C. Who should apply: Bachelors/Masters in Chemical/Biotechnology/Mechanical
Engineering or Masters in Physics. Some programming experience preferred. (1 position, FA only)
24 Venkat
Gundabala
Droplet microfluidics for high-throughput studies on C. elegans: Caenorhabditis elegans (C. elegans) is a nematode
commonly used as a model organismfor molecular and developmental biology studies. With about 60% of its genes
having human homologs, coupled with its transparent body, and ease of culturing, C. elegans is an attractive choice for
biologists. Droplet microfluidics is currently emerging as an ideal tool in cell biology (single cell encapsulation for cell-
based studies, etc.), bio-medicine (microencapsulation of cells onto particles, etc.), amongst other fields. In this project
we will use droplet-based microfluidics to study the behavioural aspects of C. elegans. The project involves developing
microfluidic devices that generate double emulsion droplets into which worm encapsulation can be done. The double
emulsion droplet will be used for chemotaxis studies on the encapsulated worm. Who should apply: Past experience in
experimental research on cell/microorganism based studies is required; Keen interest on doing experiments is a must;
engineering background or prior exposure to the area of microfluidics would be a plus. (1 position, TAP/FA)
25 Ratul Dasgupta Interfacial flows: Have you ever wondered why a jet of water breaks up into tiny droplets. Do you know how tiny drops
of rain spread, after hitting our windows. Do all droplets spread in the same way? What would happen if we made the
dropletslarge, or the surface very rough? What if, the droplets fell one after the other? What determines the shape
of a puddle of water lying on our floor? What is that intricate pattern of waves that appear around a stone lying in a
moving stream? If you enjoy thinking about fluid mechanics problems, read on! This is an opportunity to pursue a PhD on
interfacial flows (see Figs. 1(a) & 1(b) for some fun pictures.). We will study impingement of a train of droplets on rigid
surfaces & understand the complexities of the spreading process, theoretically & computationally. The candidate will
participate in code development and use numerical tools in combination with theoretical techniques. There could be an
opportunity to also work on experiments later.
Who should apply: Basic knowledge of fluid mechanics at an undergraduate or graduate level is necessary. If you enjoy
learning computational techniques and writing codes, that will be a big advantage. Good abilities in mathematics &
physics, while not absolutely necessary, will definitely help. Most importantly, you should enjoy doing and being in
research. If interested, please apply. You can also write to me at dasgupta.ratul@gmail.com (1 position, TAP/FA)
26 Partha S.
Goswami
Dynamics of inertial suspension in confined geometry: experiments and modeling: The project deals with the
theoretical and experimental investigation of the dynamics of inertial suspension in micro/milli channels. In general
small scale (like microfluidic) devices operate at very low flow rates, which lead the common idea that in case of flow
in microchannel, fluid inertia does not play significant role. But during the motion in confined channel the constituent
particle of suspension experiences inertial lift force, which in turn produces particle migration. External parameters which
control the magnitude and the direction of the lift forces include the channel dimensions, particle diameter, shape of
the particles, and fluid flow rates. Such migration behavior of the particle can be utilized to develop filter-less separation
technology based on particle shape and size. Investigation in this area also provide insight in designing the micro-reactors
which deals with particle laden flows. Here we plan to apply fully resolved lattice Boltzmann method (LBM) (advanced
CFD technique) to numerically simulate the dynamics of particle and fluid flow behavior, considering interparticle
interactions as well. Furthermore the study will be extended to investigate the migration behavior of non-spherical
particles.
Experiments will be conducted using in-house-developed micro-PIV technique to validate the theoretical results
and to demonstrate the conditions required for particle separation in fluid-particle suspensions. The results and the
insight gained from the proposed study would help in more scientific design and development of filter-less separation
technology which can be applied to chemical and biotechnological processes. (Ref: Physical Review Letters(2009), 102(9),
094503).
Who should apply: Background-Chemical/Mechanical/Physics; should have ability to write program in C/C++/Fortran etc.
Should be motivated enough to take up challenges of experimental difficulties.
For clarifications write me at psg@che.iitb.ac.in (1 position, TAP/FA)
27 Partha S.
Goswami
Dynamics of Particle Laden Turbulent Suspensions- Direct numerical simulation (DNS): Particle laden turbulent flows
find applications in many industrial processes such as energy conversion, air pollution control, pneumatic conveying of
solids, fluidized bed reactors etc. In these types of flows, there are strong coupling between the turbulent fluctuations in
the fluid phase and the fluctuating velocities of the particles. Owing to this simultaneous analysis of both the phases give
insight to the modeling of transport processes in large scale engineering systems. Due to the complexity of the physics
behind dense particulate flows, the current modeling paradigm mainly depends on empirical correlations that require
fine-tuning with the aid of experimental data. As a consequence, these over-simplified models lack the capability of
quantitative prediction of the dynamical behavior and also require frequent experimental validations. Such limitations are
the main hurdles in advanced computational modeling of these reactors.
The goal of the research is to carry out direct numerical simulations (DNS) and also to develop models based on the
physical insight obtained from direct numerical simulations (DNS). The specific steps are as follows.
1. Development of advanced methods for two way coupled direct numerical simulation (DNS) of moderately dense
particle laden turbulent flows, enabling highly accurate simulations which are applicable for fluidized bed reactors and
numerous energy conversion devices.
2. Investigation of the fluid phase and particle phase behaviour using fully particle resolved simulations, which is
applicable when the particle size is larger the the size of the smallest scale of the turbulence.
3. Developing the models based on the physical insight obtained from fully resolved direct numerical simulations. Such
a model will address both the issues of like effect of turbulence on particle dynamics and the turbulence modulation
due to the presence of particle phase. Ref: J. Fluid Mech. 687, 1-40 (2011). Working on this project the student will gain
knowledge in advanced CFD techniques.
Who should apply: Background: Chemical/Mechanical/Physics; should have ability to write program in C/C++/Fortran
etc. For clarifications mail me at psg@che.iitb.ac.in. (1 position, TAP/FA)
28 Partha S.
Goswami
Dynamics of particle-laden flows in complex geometries: Experiments (PIV) and Large Eddy Simulations (LES):
Particle-laden turbulent flows find applications in many industrial processes like pneumatic transport of powders,
coal combustion, fluidised bad reactors etc. Proper design of such equipments depends on detail understanding of
interaction between particle and turbulent fluid phase. Turbulence plays important role in both the distribution and de-
mixing/segregation of the particles. Depending on the intensity of the turbulence and particle inertia, higher particle
concentration may happen near the wall region of the flow geometry which may cause higher rate of particle deposition
at the wall. Similarly particle also plays important role on modulation of turbulence. Therefore the interaction is two-way.
A proper understanding will lead to the assessment of deposition behavior and the transport coefficients in the above
mentioned processes. The interaction is complex in nature due to the presence of multiple length and time- scales for
both the particle and fluid phase.
In the proposed project we plan to conduct experiments and simulations to predict dynamics of both the phases
simultaneously starting from simple to complex geometries. Simulation will be performed based on fluid-particle coupled
model (two way coupling) to investigate the dynamics of both the phases. we plan to couple large eddy simulation
(LES) for fluid phase with discrete element model (DEM) for particle phase to understand the dynamics of turbulent
suspensions with higher solid loading. Effect of subgrid scale modeling on the two phase statistics for different Reynolds
number, particle inertia, and particle loading will be investigated. Experiments will be conducted in a vertical flow
geometries using particle image velocimetry (PIV) to validate the theoretical results. Ref: J. Fluid Mech. 687, 41-71 (2011).
Working on this project the student will gain knowledge in advanced CFD and experimental techniques.
Who should apply: Background-Chemical/Mechanical/Physics, Either should have ability to write program in C/C++/
Fortran etc. Or should be motivated enough to take up challenges of experimental difficulties.
For details mail at psg@che.iitb.ac.in (1 position, TAP/FA)
29 Pramod
Wangikar
Metabolic Engineering of Cyanobacteria for enhanced biofuel production. Algal biofuels provide an attractive alternative
to other forms of biofuels such as those derived from terrestrial biomass. Importantly, algae can grow on barren land and
with wastewater or salt water and therefore, do not compete with food or animal feed crops. Algae, particularly blue-
green algae or cyanobacteria, provide much higher photosynthesis efficiencies compared to plants and have the potential
to capture a larger fraction of the incident solar energy. Cyanobacteria are a group of photosynthetic prokaryotes that are
credited for their role in converting the anoxic environment to the current oxic environment. Although cyanobacteria do
not produce lipid in the form of storage molecules, they can be engineered to produce other more readily usable liquid
biofuels such as ethanol and butanol. While cyanobacterial biofuels hold promise, a technological breakthrough is needed
for improvements in biofuel productivity before their commercialization. Our group currently makes extensive use of the
metabolomics, fluxomics, transcriptomics and proteomics technologies to gain insights at molecular level, to be able to
develop detailed genome scale models and estimate the model parameters in a reliable manner. Efforts are also on to
develop effective expression systems and gene knockout strategies to implement the genetic modifications predicted by
the model. We collaborate extensively with Reliance Industries Ltd. on this project and the student will get an opportunity
to interact with the industry.As part of this project, the student will carry out model driven metabolic engineering of a
cyanobacterial strain to improve fuel productivity levels. The student will get an opportunity to construct and validate a
metabolic model and estimate the intracellular reaction rates. Metabolic model validation will involve a detailed
physiological characterization, metabolic profiles and 13C flux analysis. The student will also get an opportunity to
implement the predicted genetic changes via tools of molecular biology. Who should apply: Background in biotechnology
or biochemistry with experience in microbial physiology and molecular biology techniques. Ability to develop and simulate
mathematical models will be an advantage. (1 position, TAP/FA)
30 Pramod Engineering ketoreductase enzymes for chiral synthesis: Chiral alcohols, usually secondary alcohols, play an important
Wangikar role as intermediates in high value products of pharmaceutical importance. Among the various enzymatic routes
available for chirally selective synthesis of secondary alcohols, that involving oxidoreductase catalyzed asymmetric
reductions is a particularly powerful approach as it potentially allows 100% of the starting material to be transformed
into the desired enantiomer. In this project jointly sponsored DBT and an industry partner (Hi Tech Biosciences Ltd.,
Pune), we have chosen to work on microbial oxidoreductases. Several proof of concept studies have been reported
on this enzyme although the following challenges remain to be addressed. (i) High cost of commercial enzymes, (ii)
Low substrate specificity and stereo-selectivity of the wild-type enzyme, (iii) Substrate inhibition, (iv) Recycling of the
enzyme and co-factors. A successful commercial application therefore will require an enzyme that is highly active and
stereoselective towards the substrate of choice, tolerates high substrate concentrations, stable and amenable to recycling
and is affordable. The student will work closely with industry partner. The student will have an opportunity to work on
the following objectives:1. Improvement of the desired properties of oxidoreductase enzymes via directed evolution
including techniques such as error prone PCR, gene shuffling and controlled randomization. The student will also attempt
model based and predictive genetic engineering to improve the enzyme properties. 2. Development of cofactor recycling
system with formate dehydroganase and by using a membrane reactor. Who should apply: Background in Biochemistry
with experience in protein chemistry and molecular biology techniques. Knowledge of molecular modeling will be an
advantage. (1 position, TAP/FA)
31 Sarika Mehra
and Rajdip
Bandyopadyay
(coguide)
Therapeutic nanoparticles to counter drug resistance: Antibiotics have been critical for the dramatic rise of life
expectancy and the fight against many diseases and infections in the past fifty years. However, over the past decade,
antimicrobial resistance has emerged as a major public-health crisis Many common gram-positive and gram-negative
bacterial pathogens such as Streptococcus pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus have
become progressively more resistant to traditional antibiotics. With the emergence of multi drug-resistant and extreme
drug-resistant Mycobacterium tuberculosis strains, there is an urgent need to find novel solutions to counter this
resistance. We have used a combination of magnetite nanoparticle with first line anti-TB drug rifampicin to achieve a
synergistic effect against intrinsic drug resistance of M. smegmatis. We have also demonstrated that the nanoparticles
alter the uptake kinetics of drugs into cells. In this project we will further understand the mechanisms of uptake and
action of the nanoparticles on M. smegmatis cells using experiments and modeling. Who should apply: B.Tech/M.Tech in
Biotechnology/Chemical engineering/Molecular Biology (1 position, FA only)
32 Sarika Mehra Systems biology of antibiotic resistance: Mechanisms and Evolution through genomics: Antibiotics have been critical for
the dramatic rise of life expectancy and the fight against many diseases and infections in the past fifty years. However,
over the past decade, antimicrobial resistance has emerged as a major public-health crisis. We are using Streptomyces
coelicolor as a model to decipher the various mechanisms employed by bacteria to counter antibiotics. A transcriptomic
study using whole-genome microarrays revealed a combination of mechanisms that Streptomyces uses to counter
fluoroquinolones. Many genes were identified to potentially aid the cells in resisting high drug concentrations. In this
project, we will study the role of these genes using knock-out mutants and transcriptomics. Further, we will study the
evolution of resistance by generating hyper-resistant mutants and employing next-generation sequencing methods to
identify mutations resulting in the observed phenotype. Who should apply: B.Tech/M.Tech/M.Sc in Biotechnology/
Chemical engineering/Molecular Biology/Biochemistry Knowledge of molecular biology techniques including cloning will
be beneficial for the project. (1 position, FA only)
33 Ateeque
Malani
Study of Interfacial Properties of Nanoparticles: Metallic and non-metallic nanoparticles (NP) have been synthesized
with excellent mechanical, electrical and thermal properties, which has potential application in variety of areas. For many
applications (e.g., pickering emulsion, catalysis and theraputic applications), their surface properties, such as wetting
and dispersion, need to modified to meet the requirement of the devices. The aim of this project is to understand the
interfacial behaviour of nanoparticles (contact angle, interfacial rheology etc.) using molecular simulations and obtain
guidelines for its potential usage. Who should apply: BE (Chemical Engineering), MTech (all branches), MSc(Physics
or Chemistry), b) Should be familiar with molecular modelling methodology, should have done numerical methods at
undergraduate or postgraduate level, significant programming experience in C/C++/Fortran/Matlab or any programming
language and should be conversant with linux/unix, ability to independently analyze results and simulation data,
experience in the field of molecular modelling is desirable, excellent communication skills. (2 positions, FA only)
34 Hemant
Nanavati
Molecular Modeling of Elasticity of Spider Silk and Related Biopolymers:
Who should apply: Chemical Engg, Polymeric Materials Science, Physics (1 position, FA only)
35 Hemant
Nanavati
Multiscale Modeling of Melt Polymer and Copolymer Systems
Who should apply: Chemical Engg, Polymeric Materials Science, Physics (1 position, FA only)

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