Free energy changes and equilibrium constants 1. Calculate the standard free-energy changes of th... more Free energy changes and equilibrium constants 1. Calculate the standard free-energy changes of the following metabolically important enzyme-catalyzed reactions at 25°C and pH 7.0 from the equilibrium constants given. (a) Glutamate + oxaloacetate ↔ aspartate + α-ketoglutarate K' eq = 6.8 (b) Dihydroxyacetone phosphate ↔ glyceraldehyde-3-phosphate K' eq = 0.0475 (c) Fructose-6-phosphate + ATP ↔ F-1,6-bisphosphate + ADP K' eq = 254 2. Calculate the equilibrium constants K' eq for each of the following reactions at pH 7.0 and 25 o C, using the ∆G o ' values given: (a) Glucose-6-phosphate + H 2 O → glucose + P I ∆G o '=-13.8 kJ/mol (b) Lactose + H 2 O → glucose + galactose ∆G o '=-15.9 kJ/mol (c) Malate → fumarate + H 2 O ∆G o '= +3.1 kJ/mol 3. If a 0.1 M solution of glucose-1-phosphate is incubated with a catalytic amount of phosphoglucomutase, the glucose-1-phosphate is transformed to glucose-6-phosphate until equilibrium is established. The equilibrium concentrations are: Glucose-1-phosphate glucose-6-phosphate 4.5 X 10-3 M 9.6 X 10-2 M Calculate K' eq and ∆G o ' for this reaction at 25 o C. 4. A direct measurement of the standard free-energy change associated with the hydrolysis of ATP is technically demanding because the minute amount of ATP remaining at equilibrium is difficult to measure accurately. The value of ∆G o ' can be calculated indirectly, however, from the equilibrium constants of two other enzymatic reactions having less favorable equilibrium constants: Glucose-6-phosphate + H 2 O → glucose + Pi K' eq = 270 ATP + glucose → ADP + glucose-6-phosphate K' eq = 890 Using this information, calculate the standard free energy of hydrolysis of ATP. Assume a temperature of 25 o C.
International Journal of Wireless & Mobile Networks, 2012
ABSTRACT Proposed work is a mobility based checkpointing and trust based rollback recovery algori... more ABSTRACT Proposed work is a mobility based checkpointing and trust based rollback recovery algorithm to provide fault tolerance in Mobile Ad hoc Network (MANET). Here each mobile host maintains a count of number of clusters a mobile host traverses through, during a single checkpoint interval. A mobile host increments 'cluster-change-count' by 1, each time it leaves a cluster and joins another. Each mobile host saves a checkpoint independently if its 'cluster-change-count' exceeds a predefined threshold. This measure is important because each mobile host leaves its last checkpoint and logs at different clusters that it has visited earlier. If the mobile host fails, the time to search and collect its last checkpoint and logs gets added to the recovery time of the mobile host. In MANET, retrieval of checkpoint and logs has to be done through a number of intermediate mobile hosts because each mobile host has short area coverage, hence direct communication among distant mobile hosts is not possible. Now if any of these mobile hosts fail, depending on the nature of failure, the checkpoint or log may be lost or forwarding of them to the failed host may be delayed causing unsuccessful or delayed recovery of the failed host respectively. This can be avoided if it is ensured that the checkpoints and logs are forwarded only through trusted nodes. Trust model proposed here computes trust value of a mobile host based on four factors: failure rate, availability in network, unused energy and recommendations from neighbour mobile hosts. Simulation results show that proposed algorithm achieves low recovery cost and high recovery probability of failed mobile hosts.
International Journal of Network Security & Its Applications, 2012
An efficient fault tolerant algorithm based on movement-based secure checkpointing and logging fo... more An efficient fault tolerant algorithm based on movement-based secure checkpointing and logging for mobile computing system is proposed here. The recovery scheme proposed here combines independent checkpointing and message logging. Here we consider mobility rate of the user in checkpointing so that mobile host can manage recovery information such as checkpoints and logs properly so that a mobile host takes less recovery time after failure. Mobile hosts save checkpoints when number of hand-off exceeds a predefined hand-off threshold value. Current approaches save logs in base station. But this approach maximizes recovery time if message passing frequency is large. If a mobile host saves log in its own memory, recovery cost will be less because log retrieval time will be small after failure. But there is a probability of memory crash of a mobile host. In that case logs can not be retrieved if it is saved only in mobile node. If the failure is transient then logs can be retrieved from the memory of mobile node. Hence in this algorithm mobile hosts also save log in own memory and base station. In case of crash recovery, log will be retrieved from base station and in case of transient failure recovery logs will be retrieved from mobile host. In this algorithm recovery probability is optimized and total recovery time is reduced in comparison to existing works. Logs are very small in size. Hence saving logs in mobile hosts does not cause much memory overhead. Hand-off threshold is a function of mobility rate, message passing frequency and failure rate of mobile hosts. This algorithm describes a secure checkpointing technique as a method for providing fault tolerance while preventing information leakage through the checkpoint data.
2012 Third International Conference on Emerging Applications of Information Technology, 2012
ABSTRACT Mobile ad hoc network (MANET) is a collection of mobile nodes dynamically forming a temp... more ABSTRACT Mobile ad hoc network (MANET) is a collection of mobile nodes dynamically forming a temporary network without a centralized administration. Failure rate and security attack rate of processes running on mobile hosts in MANET is high due to its characteristics such as open network environment, dynamic topology due to random node movement, lack of centralized control, fixed infrastructure, stable storage etc. Existing secure checkpointing algorithm using cryptography to provide fault tolerance in failure and security attack prone mobile cellular network cannot be applied in MANET due to enhanced overhead. As an alternative solution, we have designed an ant colony based trust model to evaluate trust value of a mobile node in MANET. A trusted node, that will never be a malicious or selfish node, has low or negligible failure and security attack rate, high available battery power which indicates high availability in the network and high positive reference from other nodes. So checkpoint is secure in a trusted mobile node without additional overheads of cryptography. Experimental result shows that using proposed mobility and trust model based checkpointing and rollback recovery technique, maximum recovery probability of 0.93 can be achieved.
ABSTRACT The morphology of plasmonic nano-assemblies has a direct influence on optical properties... more ABSTRACT The morphology of plasmonic nano-assemblies has a direct influence on optical properties, such as localised surface plasmon resonance (LSPR) and surface enhanced Raman scattering (SERS) intensity. Assemblies with core-satellite morphologies are of particular interest, because this morphology has a high density of hot-spots, while constraining the overall size. Herein, a simple method is reported for the self-assembly of gold NPs nano-assemblies with a core-satellite morphology, which was mediated by hyperbranched polymer (HBP) linkers. The HBP linkers have repeat units that do not interact strongly with gold NPs, but have multiple end-groups that specifically interact with the gold NPs and act as anchoring points resulting in nano-assemblies with a large (~48 nm) core surrounded by smaller (~15 nm) satellites. It was possible to control the number of satellites in an assembly which allowed optical parameters such as SPR maxima and the SERS intensity to be tuned. These results were found to be consistent with finite-difference time domain (FDTD) simulations. Furthermore, the multiplexing of the nano-assemblies with a series of Raman tag molecules was demonstrated, without an observable signal arising from the HBP linker after tagging. Such plasmonic nano-assemblies could potentially serve as efficient SERS based diagnostics or biomedical imaging agents in nanomedicine.
Autophagy is an intracellular catabolic process that is required to maintain cellular homeostasis... more Autophagy is an intracellular catabolic process that is required to maintain cellular homeostasis. Pathogen-elicited host cell autophagy may favour containment of infection or may help in bacterial survival. Pathogens have developed the ability to modulate host autophagy. The secreted antigen HP0175, a peptidyl prolyl cis,trans isomerase of Helicobacter pylori, has moonlighting functions with reference to host cells. Here we show that it executes autophagy in gastric epithelial cells. Autophagy is dependent on the unfolded protein response (UPR) that activates the expression of PKR-like ER kinase (PERK). This is accompanied by phosphorylation of eukaryotic initiation factor 2α (eIF-2α) and transcriptional activation of ATF4 and CHOP. Knockdown of UPR-related genes inhibits the conversion of LC3I to LC3II, a marker of autophagy. The autophagy-inducing ability of H. pylori is compromised when cells are infected with an isogenic hp0175 mutant. Autophagy precedes apoptosis. Silencing of BECLIN1 augments cleavage of caspase 3 as well as apoptosis. Increased apoptosis of gastric epithelial cells is known to be linked to H. pylori-mediated gastric inflammation and carcinogenesis. To the best of our knowledge, this study provides the first demonstration of how HP0175 endowed with moonlighting functions links UPR-dependent autophagy and apoptosis during H. pylori infection.
Nonlinear Frequency Generation and Conversion: Materials, Devices, and Applications XII, 2013
ABSTRACT The surface plasmon enhanced ultra-low threshold second harmonic generation is observed,... more ABSTRACT The surface plasmon enhanced ultra-low threshold second harmonic generation is observed, designed and simulated in whispering gallery resonator made of MgO doped periodically poled LiNbO3. Here the electric field associated with incident optical radiation of picowatt level is amplified to milliwatt level through surface plasmon resonance in Kretschmann geometry which is formed by a BK7 prism plane, 29 nm thin gold layer and 20 nm thin GaAs layer. This enhanced electric field then coupled to a whispering gallery resonator, which facilitated the generation of second harmonic for an incident laser radiation of picowatt level. In this proposed configuration with an incident optical power of 94.6 pW, generated second harmonic through whispering gallery resonator is found to be 14.6 mW.
Plasmonic gold nanoassemblies that self-assemble with the aid of linking molecules or polymers ha... more Plasmonic gold nanoassemblies that self-assemble with the aid of linking molecules or polymers have the potential to yield controlled hierarchies of morphologies and consequently result in materials with tailored optical (e.g., localized surface plasmon resonances (LSPR)) and spectroscopic properties (e.g., surface-enhanced Raman scattering (SERS)). Molecular linkers that are structurally well-defined are promising for forming hybrid nanoassemblies which are stable in aqueous solution and are increasingly finding application in nanomedicine. Despite much ongoing research in this field, the precise role of molecular linkers in governing the morphology and properties of the hybrid nanoassemblies remains unclear. Previously we have demonstrated that branched linkers, such as hyperbranched polymers, with specific anchoring end groups can be successfully employed to form assemblies of gold NPs demonstrating near-infrared SPRs and intense SERS scattering. We herein introduce a tailored polymer as a versatile molecular linker, capable of manipulating nanoassembly morphologies and hot-spot density. In addition, this report explores the role of the polymeric linker architecture, specifically the degree of branching of the tailored polymer in determining the formation, morphology, and properties of the hybrid nanoassemblies. The degree of branching of the linker polymer, in addition to the concentration and number of anchoring groups, is observed to strongly influence the self-assembly process. The assembly morphology shifts primarily from 1D-like chains to 2D plates and finally to 3D-like globular structures, with increase in degree of branching of the macromolecular linker. Insights have been gained into how the morphology influences the SERS performance of these nanoassemblies with respect to hot-spot density. These findings supplement the understanding of the morphology determining nanoassembly formation and pave the way for the possible application of these nanoassemblies as SERS biosensors for medical diagnostics.
Free energy changes and equilibrium constants 1. Calculate the standard free-energy changes of th... more Free energy changes and equilibrium constants 1. Calculate the standard free-energy changes of the following metabolically important enzyme-catalyzed reactions at 25°C and pH 7.0 from the equilibrium constants given. (a) Glutamate + oxaloacetate ↔ aspartate + α-ketoglutarate K' eq = 6.8 (b) Dihydroxyacetone phosphate ↔ glyceraldehyde-3-phosphate K' eq = 0.0475 (c) Fructose-6-phosphate + ATP ↔ F-1,6-bisphosphate + ADP K' eq = 254 2. Calculate the equilibrium constants K' eq for each of the following reactions at pH 7.0 and 25 o C, using the ∆G o ' values given: (a) Glucose-6-phosphate + H 2 O → glucose + P I ∆G o '=-13.8 kJ/mol (b) Lactose + H 2 O → glucose + galactose ∆G o '=-15.9 kJ/mol (c) Malate → fumarate + H 2 O ∆G o '= +3.1 kJ/mol 3. If a 0.1 M solution of glucose-1-phosphate is incubated with a catalytic amount of phosphoglucomutase, the glucose-1-phosphate is transformed to glucose-6-phosphate until equilibrium is established. The equilibrium concentrations are: Glucose-1-phosphate glucose-6-phosphate 4.5 X 10-3 M 9.6 X 10-2 M Calculate K' eq and ∆G o ' for this reaction at 25 o C. 4. A direct measurement of the standard free-energy change associated with the hydrolysis of ATP is technically demanding because the minute amount of ATP remaining at equilibrium is difficult to measure accurately. The value of ∆G o ' can be calculated indirectly, however, from the equilibrium constants of two other enzymatic reactions having less favorable equilibrium constants: Glucose-6-phosphate + H 2 O → glucose + Pi K' eq = 270 ATP + glucose → ADP + glucose-6-phosphate K' eq = 890 Using this information, calculate the standard free energy of hydrolysis of ATP. Assume a temperature of 25 o C.
International Journal of Wireless & Mobile Networks, 2012
ABSTRACT Proposed work is a mobility based checkpointing and trust based rollback recovery algori... more ABSTRACT Proposed work is a mobility based checkpointing and trust based rollback recovery algorithm to provide fault tolerance in Mobile Ad hoc Network (MANET). Here each mobile host maintains a count of number of clusters a mobile host traverses through, during a single checkpoint interval. A mobile host increments 'cluster-change-count' by 1, each time it leaves a cluster and joins another. Each mobile host saves a checkpoint independently if its 'cluster-change-count' exceeds a predefined threshold. This measure is important because each mobile host leaves its last checkpoint and logs at different clusters that it has visited earlier. If the mobile host fails, the time to search and collect its last checkpoint and logs gets added to the recovery time of the mobile host. In MANET, retrieval of checkpoint and logs has to be done through a number of intermediate mobile hosts because each mobile host has short area coverage, hence direct communication among distant mobile hosts is not possible. Now if any of these mobile hosts fail, depending on the nature of failure, the checkpoint or log may be lost or forwarding of them to the failed host may be delayed causing unsuccessful or delayed recovery of the failed host respectively. This can be avoided if it is ensured that the checkpoints and logs are forwarded only through trusted nodes. Trust model proposed here computes trust value of a mobile host based on four factors: failure rate, availability in network, unused energy and recommendations from neighbour mobile hosts. Simulation results show that proposed algorithm achieves low recovery cost and high recovery probability of failed mobile hosts.
International Journal of Network Security & Its Applications, 2012
An efficient fault tolerant algorithm based on movement-based secure checkpointing and logging fo... more An efficient fault tolerant algorithm based on movement-based secure checkpointing and logging for mobile computing system is proposed here. The recovery scheme proposed here combines independent checkpointing and message logging. Here we consider mobility rate of the user in checkpointing so that mobile host can manage recovery information such as checkpoints and logs properly so that a mobile host takes less recovery time after failure. Mobile hosts save checkpoints when number of hand-off exceeds a predefined hand-off threshold value. Current approaches save logs in base station. But this approach maximizes recovery time if message passing frequency is large. If a mobile host saves log in its own memory, recovery cost will be less because log retrieval time will be small after failure. But there is a probability of memory crash of a mobile host. In that case logs can not be retrieved if it is saved only in mobile node. If the failure is transient then logs can be retrieved from the memory of mobile node. Hence in this algorithm mobile hosts also save log in own memory and base station. In case of crash recovery, log will be retrieved from base station and in case of transient failure recovery logs will be retrieved from mobile host. In this algorithm recovery probability is optimized and total recovery time is reduced in comparison to existing works. Logs are very small in size. Hence saving logs in mobile hosts does not cause much memory overhead. Hand-off threshold is a function of mobility rate, message passing frequency and failure rate of mobile hosts. This algorithm describes a secure checkpointing technique as a method for providing fault tolerance while preventing information leakage through the checkpoint data.
2012 Third International Conference on Emerging Applications of Information Technology, 2012
ABSTRACT Mobile ad hoc network (MANET) is a collection of mobile nodes dynamically forming a temp... more ABSTRACT Mobile ad hoc network (MANET) is a collection of mobile nodes dynamically forming a temporary network without a centralized administration. Failure rate and security attack rate of processes running on mobile hosts in MANET is high due to its characteristics such as open network environment, dynamic topology due to random node movement, lack of centralized control, fixed infrastructure, stable storage etc. Existing secure checkpointing algorithm using cryptography to provide fault tolerance in failure and security attack prone mobile cellular network cannot be applied in MANET due to enhanced overhead. As an alternative solution, we have designed an ant colony based trust model to evaluate trust value of a mobile node in MANET. A trusted node, that will never be a malicious or selfish node, has low or negligible failure and security attack rate, high available battery power which indicates high availability in the network and high positive reference from other nodes. So checkpoint is secure in a trusted mobile node without additional overheads of cryptography. Experimental result shows that using proposed mobility and trust model based checkpointing and rollback recovery technique, maximum recovery probability of 0.93 can be achieved.
ABSTRACT The morphology of plasmonic nano-assemblies has a direct influence on optical properties... more ABSTRACT The morphology of plasmonic nano-assemblies has a direct influence on optical properties, such as localised surface plasmon resonance (LSPR) and surface enhanced Raman scattering (SERS) intensity. Assemblies with core-satellite morphologies are of particular interest, because this morphology has a high density of hot-spots, while constraining the overall size. Herein, a simple method is reported for the self-assembly of gold NPs nano-assemblies with a core-satellite morphology, which was mediated by hyperbranched polymer (HBP) linkers. The HBP linkers have repeat units that do not interact strongly with gold NPs, but have multiple end-groups that specifically interact with the gold NPs and act as anchoring points resulting in nano-assemblies with a large (~48 nm) core surrounded by smaller (~15 nm) satellites. It was possible to control the number of satellites in an assembly which allowed optical parameters such as SPR maxima and the SERS intensity to be tuned. These results were found to be consistent with finite-difference time domain (FDTD) simulations. Furthermore, the multiplexing of the nano-assemblies with a series of Raman tag molecules was demonstrated, without an observable signal arising from the HBP linker after tagging. Such plasmonic nano-assemblies could potentially serve as efficient SERS based diagnostics or biomedical imaging agents in nanomedicine.
Autophagy is an intracellular catabolic process that is required to maintain cellular homeostasis... more Autophagy is an intracellular catabolic process that is required to maintain cellular homeostasis. Pathogen-elicited host cell autophagy may favour containment of infection or may help in bacterial survival. Pathogens have developed the ability to modulate host autophagy. The secreted antigen HP0175, a peptidyl prolyl cis,trans isomerase of Helicobacter pylori, has moonlighting functions with reference to host cells. Here we show that it executes autophagy in gastric epithelial cells. Autophagy is dependent on the unfolded protein response (UPR) that activates the expression of PKR-like ER kinase (PERK). This is accompanied by phosphorylation of eukaryotic initiation factor 2α (eIF-2α) and transcriptional activation of ATF4 and CHOP. Knockdown of UPR-related genes inhibits the conversion of LC3I to LC3II, a marker of autophagy. The autophagy-inducing ability of H. pylori is compromised when cells are infected with an isogenic hp0175 mutant. Autophagy precedes apoptosis. Silencing of BECLIN1 augments cleavage of caspase 3 as well as apoptosis. Increased apoptosis of gastric epithelial cells is known to be linked to H. pylori-mediated gastric inflammation and carcinogenesis. To the best of our knowledge, this study provides the first demonstration of how HP0175 endowed with moonlighting functions links UPR-dependent autophagy and apoptosis during H. pylori infection.
Nonlinear Frequency Generation and Conversion: Materials, Devices, and Applications XII, 2013
ABSTRACT The surface plasmon enhanced ultra-low threshold second harmonic generation is observed,... more ABSTRACT The surface plasmon enhanced ultra-low threshold second harmonic generation is observed, designed and simulated in whispering gallery resonator made of MgO doped periodically poled LiNbO3. Here the electric field associated with incident optical radiation of picowatt level is amplified to milliwatt level through surface plasmon resonance in Kretschmann geometry which is formed by a BK7 prism plane, 29 nm thin gold layer and 20 nm thin GaAs layer. This enhanced electric field then coupled to a whispering gallery resonator, which facilitated the generation of second harmonic for an incident laser radiation of picowatt level. In this proposed configuration with an incident optical power of 94.6 pW, generated second harmonic through whispering gallery resonator is found to be 14.6 mW.
Plasmonic gold nanoassemblies that self-assemble with the aid of linking molecules or polymers ha... more Plasmonic gold nanoassemblies that self-assemble with the aid of linking molecules or polymers have the potential to yield controlled hierarchies of morphologies and consequently result in materials with tailored optical (e.g., localized surface plasmon resonances (LSPR)) and spectroscopic properties (e.g., surface-enhanced Raman scattering (SERS)). Molecular linkers that are structurally well-defined are promising for forming hybrid nanoassemblies which are stable in aqueous solution and are increasingly finding application in nanomedicine. Despite much ongoing research in this field, the precise role of molecular linkers in governing the morphology and properties of the hybrid nanoassemblies remains unclear. Previously we have demonstrated that branched linkers, such as hyperbranched polymers, with specific anchoring end groups can be successfully employed to form assemblies of gold NPs demonstrating near-infrared SPRs and intense SERS scattering. We herein introduce a tailored polymer as a versatile molecular linker, capable of manipulating nanoassembly morphologies and hot-spot density. In addition, this report explores the role of the polymeric linker architecture, specifically the degree of branching of the tailored polymer in determining the formation, morphology, and properties of the hybrid nanoassemblies. The degree of branching of the linker polymer, in addition to the concentration and number of anchoring groups, is observed to strongly influence the self-assembly process. The assembly morphology shifts primarily from 1D-like chains to 2D plates and finally to 3D-like globular structures, with increase in degree of branching of the macromolecular linker. Insights have been gained into how the morphology influences the SERS performance of these nanoassemblies with respect to hot-spot density. These findings supplement the understanding of the morphology determining nanoassembly formation and pave the way for the possible application of these nanoassemblies as SERS biosensors for medical diagnostics.
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Papers by Priyanka Dey