Hydrodynamic shielding induced stability of zipping macromolecules in elongational flows

Agarwal, US Uday; Mashelkar, R. A.

doi:10.1063/1.467116

Cited by 18 publications

(12 citation statements)

References 32 publications

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“…Indeed, differences in the levels of association in diverse protein systems dictate the different degrees of shielding, especially of hydrophobic residues concealed in the protein matrix, from hydrodynamic drag during shear flow. 83,84 Hence, it is difficult to obtain uniform data to allow the formulation of a theoretical model relating protein conformation to shear. For these reasons, dilute solutions of homopolymers, especially unbranched polymer chains, have been used as model systems for shear studies because of their inherent structural uniformity.…”

Section: Molecular Models and Theoretical Aspectsmentioning

confidence: 99%

The effects of shear flow on protein structure and function

Bekard

Asimakis

Bertolini³

et al. 2011

Biopolymers

172

140

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Toxoplasma gondii usually causes an asymptomatic and then latent infection in human adults; however, a potentially fatal disseminated form can occur in immunocompromised patients. Given that the diagnosis of acute Toxoplasma infection, as opposed to latent disease, relies on finding direct evidence of T. gondii infection in tissue, pathologic examination is critical. There have only been a few reports describing the cytomorphology of Toxoplasma in exfoliative cytology, and no reports of the findings in Thin Prep. In this report, we describe a fatal case of toxoplasmosis in a cardiac transplant patient that was diagnosed by respiratory cytopathology. Although the extracellular organisms were well visualized on the Wright‐Giemsa stained cytospin, they were only faintly seen on the Pap‐stained cytospin trapped within mucin and were not easily appreciated on the ThinPrep slides nor the H&E stained cell block sections. An immunohistochemical stain for Toxoplasma performed on the cell block was strongly positive, and an autopsy performed on the patient confirmed disseminated infection. Our case illustrates that the diagnosis of Toxoplasma in exfoliative cytology specimens can be challenging since organisms are not well visualized on ThinPrep or Pap‐stained material; therefore, Wright‐Giemsa stained material can be particularly helpful. Diagn. Cytopathol. 2012. © 2011 Wiley Periodicals, Inc.

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Section: Molecular Models and Theoretical Aspectsmentioning

confidence: 99%

The effects of shear flow on protein structure and function

Bekard

Asimakis

Bertolini³

et al. 2011

Biopolymers

172

140

View full text Add to dashboard Cite

show abstract

“…1,2 Similarly, fully stretched polymer molecules have drawn interest in relation to chain scission behavior in strong flows. [3][4][5] Further, many rheology modifying applications such as turbulent drag reduction and enhanced oil recovery are based on the flow induced stretching process of dissolved polymer coils, and the influence of the deformed polymer chains on solution rheology. 1,2 In this paper we use Brownian dynamics simulation to examine the coil-stretch transition of polymers, and the hysteresis therein.…”

Section: Introductionmentioning

confidence: 99%

Brownian dynamics simulation of a polymer molecule in solution under elongational flow

Agarwal¹,

Bhargava²,

Mashelkar³

1998

The Journal of Chemical Physics

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We use Brownian dynamics simulation to study coil-stretch transition of macromolecules in solution. Into a simple elongational flow field, we introduce freely jointed bead-rod chain model molecules in their coiled and stretched states, and follow the conformational changes. We find good agreement of our simulation results with the available theoretical predictions for low and high strain rates (⑀ ). At the intermediate elongation rates ͑near the onset of coil-stretch transition͒ of the flow field, we find that the residence time required for stretching of an initially coiled chain can be extremely large as compared to predicted (1ϩln(ͱN))⑀ Ϫ1, especially for the non-free-draining case. Hence, the chain conformation is dependent on the initial state of the chain molecule for residence time as long as 100⑀Ϫ1 . Thus, hysteresis is predicted when chain residence time in such an elongational flow field is limited, as in practical situations. Further, at such intermediate ⑀ , the chain molecule is seen to undergo Brownian fluctuation induced jumps between a randomly coiled state and another partially stretched state. This suggests the existence of more than one equilibrium conformation that is unstable to Brownian fluctuations.

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“…The extent of chain stretching is also important in determining the chain scission tendency during strong flows. [4][5][6][7] Extensional flows at (⑀ Ͼ⑀ cs ) often involve the polymer molecules experiencing the stretching forces for a limited time or strain. If this strain is not sufficient for complete stretching of the polymer molecules, then the solution rheology is dependent on the extent and rate of stretching, and hence on the strain history of the solution.…”

Section: Introductionmentioning

confidence: 99%

Effect of initial conformation, flow strength, and hydrodynamic interaction on polymer molecules in extensional flows

Agarwal

2000

The Journal of Chemical Physics

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Brownian dynamics simulations are used to study the unraveling process of polymer molecules in dilute solutions under strong elongational flows. We follow chain extension, segmental alignment, and viscosity contribution behavior of individual, randomly coiled, freely jointed bead-rod chain model molecules. In the absence of hydrodynamic shielding, segmental orientation at an intermediate strain rate begins only when aided by overall chain extension. However, at a very high strain rate, rapid initial segmental orientation and lateral chain compression precedes overall chain extension, resulting in the formation of sharp folds in most chains. Fold formation during the extension process is characterized by a sudden decrease in the rate of overall chain extension, an intermediate plateau in birefringence, and a disproportionately low chain end-to-end distance. Hydrodynamic screening generally slows down the uncoiling process, sometimes enough to avoid the formation of folded conformations.

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Hydrodynamic shielding induced stability of zipping macromolecules in elongational flows

Cited by 18 publications

References 32 publications

The effects of shear flow on protein structure and function

The effects of shear flow on protein structure and function

Brownian dynamics simulation of a polymer molecule in solution under elongational flow

Effect of initial conformation, flow strength, and hydrodynamic interaction on polymer molecules in extensional flows

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