Biomolecular structures are held together by a complex network of molecular interactions that dir... more Biomolecular structures are held together by a complex network of molecular interactions that direct assembly and stabilize structures. In order to translate the
Biomolecular structures are held together by a complex network of molecular interactions that dir... more Biomolecular structures are held together by a complex network of molecular interactions that direct assembly and stabilize structures. In order to translate the fundamental molecular interactions of biomolecules into the design of functional biomaterials, we have developed a model system that integrates nucleic acids and self-assembling peptides (shown below). These nucleopeptides serve as a smallmodel system for the study of the non-covalent molecular interactions involved in biomolecule self-assembly measured through impedance. The peptides are in this case our system of electronic circuit. The emergent electronic properties found in most of our 21 samples, which were measured by Electrical Impedance Spectroscopy (EIS) and analyzed by ZMAN software shows promise. This is because one of the most frequent application to show up was Battery and Supercapacitor which can be used in Biosensors. Abstract
INTERACTION BETWEEN NUCLEOSIDE DIPHOSPHATE KINASE AND GRAPHENE OXIDE AND ITS IMPACT ON CARDIOVASC... more INTERACTION BETWEEN NUCLEOSIDE DIPHOSPHATE KINASE AND GRAPHENE OXIDE AND ITS IMPACT ON CARDIOVASCULAR DISEASES Here we report possibly for the first time the computational understanding of the interactions between the nanomaterial Graphene Oxide (GO) and the enzyme Nuclear Diphosphate Kinase (NDPK) and its implications. Nanoscale Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) were used to run simulations and analyze the interactions between NDPK and GO. The simulations have run for 100 ns, and it is observed that GO is able to block the active site of the enzyme. Graphene oxide is being used because of its excellent biocompatibility, high water dispersibility, and large surface area [3]. NDPK has numerous roles in the body, such as activating G-proteins and transferring a phosphate from ATP to GDP (resulting in ADP and GTP). It also plays a role in cell proliferation, development, signal transduction, endocytosis, etc[2]. Normally, increased activity of NDPK yields th...
Ishita Choudhury, Prabir Patra, and Alicia Petryk's poster on a method to separate cells base... more Ishita Choudhury, Prabir Patra, and Alicia Petryk's poster on a method to separate cells based on intracellular magnetic iron oxide nanoparticles concentration to allow for further study and optimize cellular uptake in tumor cells.
It is estimated that about 30% of the colorectal cancer (CRC) cases are hereditary and related to... more It is estimated that about 30% of the colorectal cancer (CRC) cases are hereditary and related to known syndromes, particularly Lynch Syndrome. This study aims to understand the molecular interactions between a mismatch repair protein, MutS and a mismatched DNA through a DNA-graphene-polypyrole (DGP) biosensor and molecular dynamics. Electrochemical impedance spectroscopy (EIS) analysis of the DGP biosensor confirms the adsorption of the DNA probe and its interactions with MutS. These results are supported by a set of all-atom molecular dynamics simulations using NAMD and CHARMM force fields. Within the first 200ns of the molecular interactions between MutS and mismatched DNA, we portray the conformational changes of the human MutS protein as it binds to the DNA. It is further found that within the first 50ns, the reactive site on the MutS protein (residues 1 to 124) start to favorably interact with the DNA for the onset of the scan cycle. This investigation additionally provides crucial insights into the interactive energetic events at the interface of MutS and the DNA through non-binding energies, thereby mapping out the events during scanning and locating the mismatch.
The study of DNA binding with nanoparticles and their packaging assembly is an essential requirem... more The study of DNA binding with nanoparticles and their packaging assembly is an essential requirement for gene therapy. The structural features of DNA and nanoparticles would be very useful in development of novel gene therapy in genes. Plants being good test system as they are tolerant of being bombarded with small particulates and usually grow normally even after such treatments. We used primers from plant named "Frigida".
A Novel Nano-biosensor for Colorectal Cancer Diagnostics by Detecting DNA Mismatch Repair Protein... more A Novel Nano-biosensor for Colorectal Cancer Diagnostics by Detecting DNA Mismatch Repair Proteins Cancer currently stands as the second-leading cause of death worldwide. Studies reveal colorectal cancer (CRC) to be the 4th leading cause of mortality due to cancer. It is estimated that about 30% of CRC cases are hereditary, of which 5% are attributed by known syndromes, particularly Lynch Syndrome. Lynch Syndrome (LS) is caused by loss or malfunction of proteins responsible for DNA mismatch repair proteins (MMR), mostly MLH1 and MSH2, causing increased risks of developing CRC. Despite the small percentage accounted with the disease, the severity of the illness still remains immense since 80% of these patients eventually develop CRC and an overwhelming 40-60 % of female patients develop endometrial cancer, the major form of cancer in women in the developing nations. This pilot study aims to fabricate a DNA-graphene-polypyrole (DGP) based biosensor to diagnose deficiency of functional...
Dispersion of single walled carbon nanotube in water is hard to achieve due to the strong cohesiv... more Dispersion of single walled carbon nanotube in water is hard to achieve due to the strong cohesive forces existing between them. A good dispersion of
Magnetotactic bacteria are a type of prokaryotic cells that can orient and migrate along the geom... more Magnetotactic bacteria are a type of prokaryotic cells that can orient and migrate along the geomagnetic field lines in order to fulfill their physiological functions and anaerobic/microaerophilic requirements. This work investigates the magnetotaxis (sensitivity to magnetic field) of Magnetospirillum magneticum and studies the ability to apply this function to very large scale integration (VLSI) design and fabrication. It is known that magnetotaxis is closely associated with a chain of magnetic particles inside the bacterial cell that acts as a dipole. MATLAB analysis and modeling as well as control of a mesh of current carrying conductors using Mentor Graphics indicate that there is a possibility of these bacteria being manipulated (through their shapes, sizes and speeds) to use them as "skilled workers" to transport one or more atoms/molecules in order to form a nano-scale, bottom-up construction methodology beneficial to the field of integrated circuit fabrication. A f...
With the rapid economic growth in developing countries, the air pollution is becoming more and mo... more With the rapid economic growth in developing countries, the air pollution is becoming more and more serious. The air in some big cities becomes foggy due to various pollution sources. Particulate matter with diameter of 2.5 microns or less is especially dangerous because they can be inhaled into deep part of lung tissues and eventually absorbed into blood circulation system. This is very harmful for human health, leading to lung cancer and other related diseases. It is important for people to have a handheld PM2.5 sensor to monitor the air pollution to decide whether they should travel or do exercises outdoor. In this research, a miniaturized PM2.5 particulate sensor based on optical sensing is proposed. The air sample flows through a chamber with constant flow rate. Incident laser light pass through the chamber and is reflected by a set of mirrors for multiple times. The light is scattered by the PM2.5 particles in the air sample so that the light intensity is weakened. The higher ...
2019 IEEE Long Island Systems, Applications and Technology Conference (LISAT), 2019
Polycaprolactone (PCL) is a material widely used in regenerative medicine because of biocompatibi... more Polycaprolactone (PCL) is a material widely used in regenerative medicine because of biocompatibility, biodegradability, and low toxicity. Applications of PCL are mainly focused on tissue engineering, wound healing, drug encapsulation and delivery etc. PCL scaffolds have been used for stem cell differentiation into various cellular lineages. However, the hydrophobicity of PCL scaffolds possess some limitation to cellular attachment. Graphene which is a single sheet of sp2 hybridized carbon atoms can enhance cellular attachment by establishing π-π interaction. Here we investigate the interaction of PCL and graphene by molecular dynamics simulation and hence fabrication of PCL scaffolds with graphene nano-inclusions for neuronal differentiation. Correlated conformational and energetic analysis are implemented. During 10ns simulation, randomly assigned PCL chains adsorbed onto the surface of graphene and the size of PCL also tended to fit graphene sheet. Wrapping phenomenon was detected after 10ns interaction. The dominant force is Van der Waal's force and hydrophobic interaction.
Aim: To differentiate mesenchymal stem cells into functional dopaminergic neurons using an electr... more Aim: To differentiate mesenchymal stem cells into functional dopaminergic neurons using an electrospun polycaprolactone (PCL) and graphene (G) nanocomposite. Methods: A one-step approach was used to electrospin the PCL nanocomposite, with varying G concentrations, followed by evaluating their biocompatibility and neuronal differentiation. Results: PCL with exiguous graphene demonstrated an ideal nanotopography with an unprecedented combination of guidance stimuli and substrate cues, aiding the enhanced differentiation of mesenchymal stem cells into dopaminergic neurons. These newly differentiated neurons were seen to exhibit unique neuronal arborization, enhanced intracellular Ca2+influx and dopamine secretion. Conclusion: Having cost-effective fabrication and room-temperature storage, the PCL-G nanocomposites could pave the way for enhanced neuronal differentiation, thereby opening a new horizon for an array of applications in neural regenerative medicine.
Vaccination is a safe and effective approach to prevent deadly diseases. To increase vaccine prod... more Vaccination is a safe and effective approach to prevent deadly diseases. To increase vaccine production, we propose that a mechanical stimulation can enhance protein production. In order to prove this hypothesis, Sf9 insect cells were used to evaluate the increase in the expression of a fusion protein from hepatitis B virus (HBV S1/S2). We discovered that the ultrasound stimulation at a frequency of 1.5 MHz, intensity of 60 mW/cm2, for a duration of 10 minutes per day increased HBV S1/S2 by 27%. We further derived a model for transport through a cell membrane under the effect of ultrasound waves, tested the key assumptions of the model through a molecular dynamics simulation package, NAMD (Nanoscale Molecular Dynamics program) and utilized CHARMM force field in a steered molecular dynamics environment. The results show that ultrasound waves can increase cell permeability, which, in turn, can enhance nutrient / waste exchange thus leading to enhanced vaccine production. This finding ...
Proceedings of the 2014 Zone 1 Conference of the American Society for Engineering Education, 2014
MEMS are typically defined as the devices or systems which are integrated with electrical and mec... more MEMS are typically defined as the devices or systems which are integrated with electrical and mechanical components on a silicon substrate through the microfabrication techniques. Due to its low cost, small size, low power consumption with high efficiency, MEMS technology has been widely used in many fields. In this paper, the design and simulation of a magnetic micropump with tri-membrane fully differential structure is presented. The proposed micropump has two inlets and two outlets. It has two pumping chambers sealed by three Si membranes. A permanent magnet is deposited on the middle membrane. Poly-Si coils are deposited on the top and bottom membranes separately. When electrical current is conducted in the coil, a magnetic field is excited, and its polarity (north and south poles) can be easily exchanged by reversing the conducting current. The design and analysis of the micropump has been discussed in details, and based on those theoretical analysis, a set of optimized design parameter has been achieved. The ANSYS simulation is used to verify the function of micropump. The proposed micropump leads to improved pumping rate with better efficiency.
Zinc finger nucleases (ZFNs) are associated with cell death and apoptosis by binding at countless... more Zinc finger nucleases (ZFNs) are associated with cell death and apoptosis by binding at countless undesired locations. This cytotoxicity is associated with the binding ability of engineered zinc finger domains to bind dissimilar DNA sequences with high affinity. In general, binding preferences of transcription factors are associated with significant degenerated diversity and complexity which convolutes the design and engineering of precise DNA binding domains. Evolutionary success of natural zinc finger proteins, however, evinces that nature created specific evolutionary traits and strategies, such as modularity and rank-specific recognition to cope with binding complexity that are critical for creating clinical viable tools to precisely modify the human genome. Our findings indicate preservation of general modularity and significant alteration of the rank-specific binding preferences of the three-finger binding domain of transcription factor SP1 when exchanging amino acids in the 2...
2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2012
Imaging is currently performed in oncologic patients for staging. Images are evaluated by radiolo... more Imaging is currently performed in oncologic patients for staging. Images are evaluated by radiologist and lesions with the liver are detected manually. Currently there is no software available which is able to detect and measure tumor volumes automatically. We are developing a software that may be able to detect tumor and give volumetric measurements automatically. Using this software a radiologist may be able to compare computer generated volumetric data in serial imaging of the patients over time, which may help in assessing progression or regression of disease and help in treatment planning.
As the electronics industry is integrating more molecules to achieve ultra-high efficiency and de... more As the electronics industry is integrating more molecules to achieve ultra-high efficiency and device density, many promising candidates like rotaxanes emerged either in conjunction with or as an alternative to conventional semiconducting materials.
Biomolecular structures are held together by a complex network of molecular interactions that dir... more Biomolecular structures are held together by a complex network of molecular interactions that direct assembly and stabilize structures. In order to translate the
Biomolecular structures are held together by a complex network of molecular interactions that dir... more Biomolecular structures are held together by a complex network of molecular interactions that direct assembly and stabilize structures. In order to translate the fundamental molecular interactions of biomolecules into the design of functional biomaterials, we have developed a model system that integrates nucleic acids and self-assembling peptides (shown below). These nucleopeptides serve as a smallmodel system for the study of the non-covalent molecular interactions involved in biomolecule self-assembly measured through impedance. The peptides are in this case our system of electronic circuit. The emergent electronic properties found in most of our 21 samples, which were measured by Electrical Impedance Spectroscopy (EIS) and analyzed by ZMAN software shows promise. This is because one of the most frequent application to show up was Battery and Supercapacitor which can be used in Biosensors. Abstract
INTERACTION BETWEEN NUCLEOSIDE DIPHOSPHATE KINASE AND GRAPHENE OXIDE AND ITS IMPACT ON CARDIOVASC... more INTERACTION BETWEEN NUCLEOSIDE DIPHOSPHATE KINASE AND GRAPHENE OXIDE AND ITS IMPACT ON CARDIOVASCULAR DISEASES Here we report possibly for the first time the computational understanding of the interactions between the nanomaterial Graphene Oxide (GO) and the enzyme Nuclear Diphosphate Kinase (NDPK) and its implications. Nanoscale Molecular Dynamics (NAMD) and Visual Molecular Dynamics (VMD) were used to run simulations and analyze the interactions between NDPK and GO. The simulations have run for 100 ns, and it is observed that GO is able to block the active site of the enzyme. Graphene oxide is being used because of its excellent biocompatibility, high water dispersibility, and large surface area [3]. NDPK has numerous roles in the body, such as activating G-proteins and transferring a phosphate from ATP to GDP (resulting in ADP and GTP). It also plays a role in cell proliferation, development, signal transduction, endocytosis, etc[2]. Normally, increased activity of NDPK yields th...
Ishita Choudhury, Prabir Patra, and Alicia Petryk's poster on a method to separate cells base... more Ishita Choudhury, Prabir Patra, and Alicia Petryk's poster on a method to separate cells based on intracellular magnetic iron oxide nanoparticles concentration to allow for further study and optimize cellular uptake in tumor cells.
It is estimated that about 30% of the colorectal cancer (CRC) cases are hereditary and related to... more It is estimated that about 30% of the colorectal cancer (CRC) cases are hereditary and related to known syndromes, particularly Lynch Syndrome. This study aims to understand the molecular interactions between a mismatch repair protein, MutS and a mismatched DNA through a DNA-graphene-polypyrole (DGP) biosensor and molecular dynamics. Electrochemical impedance spectroscopy (EIS) analysis of the DGP biosensor confirms the adsorption of the DNA probe and its interactions with MutS. These results are supported by a set of all-atom molecular dynamics simulations using NAMD and CHARMM force fields. Within the first 200ns of the molecular interactions between MutS and mismatched DNA, we portray the conformational changes of the human MutS protein as it binds to the DNA. It is further found that within the first 50ns, the reactive site on the MutS protein (residues 1 to 124) start to favorably interact with the DNA for the onset of the scan cycle. This investigation additionally provides crucial insights into the interactive energetic events at the interface of MutS and the DNA through non-binding energies, thereby mapping out the events during scanning and locating the mismatch.
The study of DNA binding with nanoparticles and their packaging assembly is an essential requirem... more The study of DNA binding with nanoparticles and their packaging assembly is an essential requirement for gene therapy. The structural features of DNA and nanoparticles would be very useful in development of novel gene therapy in genes. Plants being good test system as they are tolerant of being bombarded with small particulates and usually grow normally even after such treatments. We used primers from plant named "Frigida".
A Novel Nano-biosensor for Colorectal Cancer Diagnostics by Detecting DNA Mismatch Repair Protein... more A Novel Nano-biosensor for Colorectal Cancer Diagnostics by Detecting DNA Mismatch Repair Proteins Cancer currently stands as the second-leading cause of death worldwide. Studies reveal colorectal cancer (CRC) to be the 4th leading cause of mortality due to cancer. It is estimated that about 30% of CRC cases are hereditary, of which 5% are attributed by known syndromes, particularly Lynch Syndrome. Lynch Syndrome (LS) is caused by loss or malfunction of proteins responsible for DNA mismatch repair proteins (MMR), mostly MLH1 and MSH2, causing increased risks of developing CRC. Despite the small percentage accounted with the disease, the severity of the illness still remains immense since 80% of these patients eventually develop CRC and an overwhelming 40-60 % of female patients develop endometrial cancer, the major form of cancer in women in the developing nations. This pilot study aims to fabricate a DNA-graphene-polypyrole (DGP) based biosensor to diagnose deficiency of functional...
Dispersion of single walled carbon nanotube in water is hard to achieve due to the strong cohesiv... more Dispersion of single walled carbon nanotube in water is hard to achieve due to the strong cohesive forces existing between them. A good dispersion of
Magnetotactic bacteria are a type of prokaryotic cells that can orient and migrate along the geom... more Magnetotactic bacteria are a type of prokaryotic cells that can orient and migrate along the geomagnetic field lines in order to fulfill their physiological functions and anaerobic/microaerophilic requirements. This work investigates the magnetotaxis (sensitivity to magnetic field) of Magnetospirillum magneticum and studies the ability to apply this function to very large scale integration (VLSI) design and fabrication. It is known that magnetotaxis is closely associated with a chain of magnetic particles inside the bacterial cell that acts as a dipole. MATLAB analysis and modeling as well as control of a mesh of current carrying conductors using Mentor Graphics indicate that there is a possibility of these bacteria being manipulated (through their shapes, sizes and speeds) to use them as "skilled workers" to transport one or more atoms/molecules in order to form a nano-scale, bottom-up construction methodology beneficial to the field of integrated circuit fabrication. A f...
With the rapid economic growth in developing countries, the air pollution is becoming more and mo... more With the rapid economic growth in developing countries, the air pollution is becoming more and more serious. The air in some big cities becomes foggy due to various pollution sources. Particulate matter with diameter of 2.5 microns or less is especially dangerous because they can be inhaled into deep part of lung tissues and eventually absorbed into blood circulation system. This is very harmful for human health, leading to lung cancer and other related diseases. It is important for people to have a handheld PM2.5 sensor to monitor the air pollution to decide whether they should travel or do exercises outdoor. In this research, a miniaturized PM2.5 particulate sensor based on optical sensing is proposed. The air sample flows through a chamber with constant flow rate. Incident laser light pass through the chamber and is reflected by a set of mirrors for multiple times. The light is scattered by the PM2.5 particles in the air sample so that the light intensity is weakened. The higher ...
2019 IEEE Long Island Systems, Applications and Technology Conference (LISAT), 2019
Polycaprolactone (PCL) is a material widely used in regenerative medicine because of biocompatibi... more Polycaprolactone (PCL) is a material widely used in regenerative medicine because of biocompatibility, biodegradability, and low toxicity. Applications of PCL are mainly focused on tissue engineering, wound healing, drug encapsulation and delivery etc. PCL scaffolds have been used for stem cell differentiation into various cellular lineages. However, the hydrophobicity of PCL scaffolds possess some limitation to cellular attachment. Graphene which is a single sheet of sp2 hybridized carbon atoms can enhance cellular attachment by establishing π-π interaction. Here we investigate the interaction of PCL and graphene by molecular dynamics simulation and hence fabrication of PCL scaffolds with graphene nano-inclusions for neuronal differentiation. Correlated conformational and energetic analysis are implemented. During 10ns simulation, randomly assigned PCL chains adsorbed onto the surface of graphene and the size of PCL also tended to fit graphene sheet. Wrapping phenomenon was detected after 10ns interaction. The dominant force is Van der Waal's force and hydrophobic interaction.
Aim: To differentiate mesenchymal stem cells into functional dopaminergic neurons using an electr... more Aim: To differentiate mesenchymal stem cells into functional dopaminergic neurons using an electrospun polycaprolactone (PCL) and graphene (G) nanocomposite. Methods: A one-step approach was used to electrospin the PCL nanocomposite, with varying G concentrations, followed by evaluating their biocompatibility and neuronal differentiation. Results: PCL with exiguous graphene demonstrated an ideal nanotopography with an unprecedented combination of guidance stimuli and substrate cues, aiding the enhanced differentiation of mesenchymal stem cells into dopaminergic neurons. These newly differentiated neurons were seen to exhibit unique neuronal arborization, enhanced intracellular Ca2+influx and dopamine secretion. Conclusion: Having cost-effective fabrication and room-temperature storage, the PCL-G nanocomposites could pave the way for enhanced neuronal differentiation, thereby opening a new horizon for an array of applications in neural regenerative medicine.
Vaccination is a safe and effective approach to prevent deadly diseases. To increase vaccine prod... more Vaccination is a safe and effective approach to prevent deadly diseases. To increase vaccine production, we propose that a mechanical stimulation can enhance protein production. In order to prove this hypothesis, Sf9 insect cells were used to evaluate the increase in the expression of a fusion protein from hepatitis B virus (HBV S1/S2). We discovered that the ultrasound stimulation at a frequency of 1.5 MHz, intensity of 60 mW/cm2, for a duration of 10 minutes per day increased HBV S1/S2 by 27%. We further derived a model for transport through a cell membrane under the effect of ultrasound waves, tested the key assumptions of the model through a molecular dynamics simulation package, NAMD (Nanoscale Molecular Dynamics program) and utilized CHARMM force field in a steered molecular dynamics environment. The results show that ultrasound waves can increase cell permeability, which, in turn, can enhance nutrient / waste exchange thus leading to enhanced vaccine production. This finding ...
Proceedings of the 2014 Zone 1 Conference of the American Society for Engineering Education, 2014
MEMS are typically defined as the devices or systems which are integrated with electrical and mec... more MEMS are typically defined as the devices or systems which are integrated with electrical and mechanical components on a silicon substrate through the microfabrication techniques. Due to its low cost, small size, low power consumption with high efficiency, MEMS technology has been widely used in many fields. In this paper, the design and simulation of a magnetic micropump with tri-membrane fully differential structure is presented. The proposed micropump has two inlets and two outlets. It has two pumping chambers sealed by three Si membranes. A permanent magnet is deposited on the middle membrane. Poly-Si coils are deposited on the top and bottom membranes separately. When electrical current is conducted in the coil, a magnetic field is excited, and its polarity (north and south poles) can be easily exchanged by reversing the conducting current. The design and analysis of the micropump has been discussed in details, and based on those theoretical analysis, a set of optimized design parameter has been achieved. The ANSYS simulation is used to verify the function of micropump. The proposed micropump leads to improved pumping rate with better efficiency.
Zinc finger nucleases (ZFNs) are associated with cell death and apoptosis by binding at countless... more Zinc finger nucleases (ZFNs) are associated with cell death and apoptosis by binding at countless undesired locations. This cytotoxicity is associated with the binding ability of engineered zinc finger domains to bind dissimilar DNA sequences with high affinity. In general, binding preferences of transcription factors are associated with significant degenerated diversity and complexity which convolutes the design and engineering of precise DNA binding domains. Evolutionary success of natural zinc finger proteins, however, evinces that nature created specific evolutionary traits and strategies, such as modularity and rank-specific recognition to cope with binding complexity that are critical for creating clinical viable tools to precisely modify the human genome. Our findings indicate preservation of general modularity and significant alteration of the rank-specific binding preferences of the three-finger binding domain of transcription factor SP1 when exchanging amino acids in the 2...
2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2012
Imaging is currently performed in oncologic patients for staging. Images are evaluated by radiolo... more Imaging is currently performed in oncologic patients for staging. Images are evaluated by radiologist and lesions with the liver are detected manually. Currently there is no software available which is able to detect and measure tumor volumes automatically. We are developing a software that may be able to detect tumor and give volumetric measurements automatically. Using this software a radiologist may be able to compare computer generated volumetric data in serial imaging of the patients over time, which may help in assessing progression or regression of disease and help in treatment planning.
As the electronics industry is integrating more molecules to achieve ultra-high efficiency and de... more As the electronics industry is integrating more molecules to achieve ultra-high efficiency and device density, many promising candidates like rotaxanes emerged either in conjunction with or as an alternative to conventional semiconducting materials.
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Papers by Prabir Patra