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Ramin Golestanian - One of the best experts on this subject based on the ideXlab platform.
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Enhanced Diffusion and Chemotaxis at the Nanoscale
Accounts of Chemical Research, 2018Co-Authors: Jaime Agudo-canalejo, Pierre Illien, Tunrayo Adeleke-larodo, Ramin GolestanianAbstract:ConspectusEnzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo Enhanced Diffusion in the presence of their corresponding substrate when this substrate is uniformly distributed in solution. Moreover, if the concentration of the substrate is nonuniform, enzymes and other small molecules have been reported to show chemotaxis (biased stochastic movement in the direction of the substrate gradient), typically toward higher concentrations of this substrate, with a few exceptions. The underlying physical mechanisms responsible for Enhanced Diffusion and chemotaxis at the nanoscale, however, are still not well understood. Understanding these processes is important both for fundamental biological research, for example, in the context of spatial organization of enzymes in metabolic pathways (metabolon formation), as well as for engineering applications, such as in the design of new vehicles fo...
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Phoresis and Enhanced Diffusion Compete in Enzyme Chemotaxis.
Nano Letters, 2018Co-Authors: Jaime Agudo-canalejo, Pierre Illien, Ramin GolestanianAbstract:Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for chemotaxis that is valid for enzymes and other small molecules. Our theory includes both nonspecific interactions between enzyme and substrate as well as complex formation through specific binding between the enzyme and the substrate. We find that two distinct mechanisms contribute to enzyme chemotaxis: a diffusiophoretic mechanism due to the nonspecific interactions and a new type of mechanism due to binding-induced changes in the Diffusion coefficient of the enzyme. The latter chemotactic mechanism points toward lower substrate concentration if the substrate enhances enzyme Diffusion and toward higher substrate concentration if the substrate inhibits enzyme Diffusion. For a typical enzyme, attractive phoresis and binding-induced Enhanced Diffusion will compete against each other. We find that phoresis dominates above a critical substrate concentration, whereas binding-induced Enhanced Diffusion dominates for low substrate concentration. Our results resolve an apparent contradiction regarding the direction of urease chemotaxis observed in experiments and, in general, clarify the relation between the Enhanced Diffusion and the chemotaxis of enzymes. Finally, we show that the competition between the two distinct chemotactic mechanisms may be used to engineer nanomachines that move toward or away from regions with a specific substrate concentration.
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phoresis and Enhanced Diffusion compete in enzyme chemotaxis
Nano Letters, 2018Co-Authors: Pierre Illien, Jaime Agudocanalejo, Ramin GolestanianAbstract:Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for chemotaxis that is valid for enzymes and other small molecules. Our theory includes both nonspecific interactions between enzyme and substrate as well as complex formation through specific binding between the enzyme and the substrate. We find that two distinct mechanisms contribute to enzyme chemotaxis: a diffusiophoretic mechanism due to the nonspecific interactions and a new type of mechanism due to binding-induced changes in the Diffusion coefficient of the enzyme. The latter chemotactic mechanism points toward lower substrate concentration if the substrate enhances enzyme Diffusion and toward higher substrate concentration if the substrate inhibits enzyme Diffusion. For a typical enzyme, attractive phoresis and binding-induced Enhanced Diffusion will compete against eac...
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Exothermicity Is Not a Necessary Condition for Enhanced Diffusion of Enzymes.
Nano Letters, 2017Co-Authors: Pierre Illien, Xi Zhao, Krishna Kanti Dey, Peter J. Butler, Ayusman Sen, Ramin GolestanianAbstract:Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is Enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We perform measurements on the endothermic and relatively slow enzyme aldolase, which also shows substrate-induced Enhanced Diffusion. We propose a new physical paradigm, which reveals that the Diffusion coefficient of a model enzyme hydrodynamically coupled to its environment increases significantly when undergoing changes in conformational fluctuations in a substrate concentration dependent manner, and is independent of the overall turnover rate of the underlying enzymatic reaction. Our results show that substrate-induced Enhanced Diffusion of enzyme molecules can be explained within an equilibrium picture and that the exothermicity of the catalyzed reaction is not a necessary condition for the observation of this phenomenon.
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Enhanced Diffusion of enzymes that catalyze exothermic reactions
Physical Review Letters, 2015Co-Authors: Ramin GolestanianAbstract:Enzymes have been recently found to exhibit Enhanced Diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature (London) 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the degree of exothermicity of the catalytic reaction involved. Four mechanisms that can lead to this effect, namely, self-thermophoresis, boost in kinetic energy, stochastic swimming, and collective heating are critically discussed, and it is shown that only the last two can be strong enough to account for the observations. The resulting quantitative description is used to examine the biological significance of the effect.
Jaime Agudocanalejo - One of the best experts on this subject based on the ideXlab platform.
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phoresis and Enhanced Diffusion compete in enzyme chemotaxis
Nano Letters, 2018Co-Authors: Pierre Illien, Jaime Agudocanalejo, Ramin GolestanianAbstract:Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for chemotaxis that is valid for enzymes and other small molecules. Our theory includes both nonspecific interactions between enzyme and substrate as well as complex formation through specific binding between the enzyme and the substrate. We find that two distinct mechanisms contribute to enzyme chemotaxis: a diffusiophoretic mechanism due to the nonspecific interactions and a new type of mechanism due to binding-induced changes in the Diffusion coefficient of the enzyme. The latter chemotactic mechanism points toward lower substrate concentration if the substrate enhances enzyme Diffusion and toward higher substrate concentration if the substrate inhibits enzyme Diffusion. For a typical enzyme, attractive phoresis and binding-induced Enhanced Diffusion will compete against eac...
Pierre Illien - One of the best experts on this subject based on the ideXlab platform.
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Enhanced Diffusion and Chemotaxis at the Nanoscale
Accounts of Chemical Research, 2018Co-Authors: Jaime Agudo-canalejo, Pierre Illien, Tunrayo Adeleke-larodo, Ramin GolestanianAbstract:ConspectusEnzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo Enhanced Diffusion in the presence of their corresponding substrate when this substrate is uniformly distributed in solution. Moreover, if the concentration of the substrate is nonuniform, enzymes and other small molecules have been reported to show chemotaxis (biased stochastic movement in the direction of the substrate gradient), typically toward higher concentrations of this substrate, with a few exceptions. The underlying physical mechanisms responsible for Enhanced Diffusion and chemotaxis at the nanoscale, however, are still not well understood. Understanding these processes is important both for fundamental biological research, for example, in the context of spatial organization of enzymes in metabolic pathways (metabolon formation), as well as for engineering applications, such as in the design of new vehicles fo...
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Phoresis and Enhanced Diffusion Compete in Enzyme Chemotaxis.
Nano Letters, 2018Co-Authors: Jaime Agudo-canalejo, Pierre Illien, Ramin GolestanianAbstract:Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for chemotaxis that is valid for enzymes and other small molecules. Our theory includes both nonspecific interactions between enzyme and substrate as well as complex formation through specific binding between the enzyme and the substrate. We find that two distinct mechanisms contribute to enzyme chemotaxis: a diffusiophoretic mechanism due to the nonspecific interactions and a new type of mechanism due to binding-induced changes in the Diffusion coefficient of the enzyme. The latter chemotactic mechanism points toward lower substrate concentration if the substrate enhances enzyme Diffusion and toward higher substrate concentration if the substrate inhibits enzyme Diffusion. For a typical enzyme, attractive phoresis and binding-induced Enhanced Diffusion will compete against each other. We find that phoresis dominates above a critical substrate concentration, whereas binding-induced Enhanced Diffusion dominates for low substrate concentration. Our results resolve an apparent contradiction regarding the direction of urease chemotaxis observed in experiments and, in general, clarify the relation between the Enhanced Diffusion and the chemotaxis of enzymes. Finally, we show that the competition between the two distinct chemotactic mechanisms may be used to engineer nanomachines that move toward or away from regions with a specific substrate concentration.
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phoresis and Enhanced Diffusion compete in enzyme chemotaxis
Nano Letters, 2018Co-Authors: Pierre Illien, Jaime Agudocanalejo, Ramin GolestanianAbstract:Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for chemotaxis that is valid for enzymes and other small molecules. Our theory includes both nonspecific interactions between enzyme and substrate as well as complex formation through specific binding between the enzyme and the substrate. We find that two distinct mechanisms contribute to enzyme chemotaxis: a diffusiophoretic mechanism due to the nonspecific interactions and a new type of mechanism due to binding-induced changes in the Diffusion coefficient of the enzyme. The latter chemotactic mechanism points toward lower substrate concentration if the substrate enhances enzyme Diffusion and toward higher substrate concentration if the substrate inhibits enzyme Diffusion. For a typical enzyme, attractive phoresis and binding-induced Enhanced Diffusion will compete against eac...
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Exothermicity Is Not a Necessary Condition for Enhanced Diffusion of Enzymes.
Nano Letters, 2017Co-Authors: Pierre Illien, Xi Zhao, Krishna Kanti Dey, Peter J. Butler, Ayusman Sen, Ramin GolestanianAbstract:Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is Enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We perform measurements on the endothermic and relatively slow enzyme aldolase, which also shows substrate-induced Enhanced Diffusion. We propose a new physical paradigm, which reveals that the Diffusion coefficient of a model enzyme hydrodynamically coupled to its environment increases significantly when undergoing changes in conformational fluctuations in a substrate concentration dependent manner, and is independent of the overall turnover rate of the underlying enzymatic reaction. Our results show that substrate-induced Enhanced Diffusion of enzyme molecules can be explained within an equilibrium picture and that the exothermicity of the catalyzed reaction is not a necessary condition for the observation of this phenomenon.
D S Simons - One of the best experts on this subject based on the ideXlab platform.
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transient Enhanced Diffusion without 311 defects in low energy b implanted silicon
Applied Physics Letters, 1995Co-Authors: L H Zhang, K S Jones, P Chi, D S SimonsAbstract:Low energy and low dose B+‐implanted Si has been studied using transmission electron microscopy (TEM) and secondary ion mass spectrometry (SIMS). Czochralski‐grown (100) Si wafers were implanted with 4 keV B+ to a dose of 1×1014/cm2. Subsequently, anneals were performed between 700 and 800 °C for times between 15 s and 8 h in an ambient atmosphere of N2. SIMS results show transient Enhanced Diffusion (TED) of the boron that saturates in less than 15 min for all annealing temperatures studied. TED results in an increase in the junction depth by at least 60 nm at a 1×1016/cm3 concentration. TEM studies show that, even for the shortest times before TED is observed, {311} defects are not detected. These results imply that there may be more than one source of interstitials for TED.
S. Novak - One of the best experts on this subject based on the ideXlab platform.
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Diffusion modeling of ion implanted boron in si during rta correlation of extended defect formation and annealing with the Enhanced Diffusion of boron
Journal of The Electrochemical Society, 1993Co-Authors: H Kinoshita, G Q Lo, D L Kwong, S. NovakAbstract:Accurate modeling of the Enhanced Diffusion of boron during rapid thermal annealing has been accomplished by incorporating the effects of extended defect formation and annealing on Enhanced Diffusion into a multizone, semiempirical model. The multizone model divides the implant profile into three zones defining regions of different defects and Diffusion enhancements. The model also contains the initial Enhanced Diffusion and the transient Diffusion effects associated with the dissolution of defect clusters and the annealing of extended defects, respectively. The saturation time for transient-Enhanced Diffusion contains an exponential function of implant dose in order to model the increase in point defect generated with higher implant dose. As a result, the model accurately simulates the boron Diffusion profile over a wide range of implant doses and also shows the immobile boron peak of precipitated dopants produced during high dose implantation.