Coherent chemical kinetics as quantum walks II: Radical-pair reactions in Arabidopsis thaliana

We apply the quantum-walk approach recently proposed in arXiv:quant-ph-1506.04213 to a radical-pair reaction where realistic estimates for the intermediate transition rates are available. The well-known average hitting time from quantum walks can be adopted as a measure of how quickly the reaction occurs and we calculate this for varying degrees of dephasing in the radical pair. The time for the radical pair to react to a product is found to be independent of the amount of dephasing introduced, even in the limit of no dephasing where the transient population dynamics exhibit strong coherent oscillations. This can be seen to arise from the existence of a rate-limiting step in the reaction and we argue that in such examples, a purely classical model based on rate equations can be used for estimating the timescale of the reaction but not necessarily its population dynamics

A family of sure-success quantum algorithms for solving a generalized Grover search problem

This work considers a generalization of Grover's search problem, viz., to find any one element in a set of acceptable choices which constitute a fraction f of the total number of choices in an unsorted data base. An infinite family of sure-success quantum algorithms are introduced here to solve this problem, each member for a different range of f. The nth member of this family involves n queries of the data base, and so the lowest few members of this family should be very convenient algorithms within their ranges of validity. The even member {A}_{2n} of the family covers ever larger range of f for larger n, which is expected to become the full range 0 infinity.Comment: 8 pages, including 4 figures in 4 page

Theoretical description of a DNA-linked nanoparticle self-assembly

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA tethered nanoparticles.Comment: Accepted for publication in Physical Review Letter

A role for calcineurin in Dictyostelium discoideum phagocytosis

The Ca2+/calmodul1n-dependent protein phosphatase calcinewin is involved in the development of the cellular slime mold Dictyostelium discoideum. Because of its interactions with Ca2+, which appear to influence D. discoideum phagocytosis (Yuan and Chia, 1999, Mol. Biol. Cell 10, 220a), we undertook studies to test whether calcineurin also plays a role in Dictyostelium phagocytosis. The immunosuppressants cyclosporin A and FK506, through the formation of cyclosporin A-cyclophilin A and FK506- FK506-binding protein complexes, respectively, inhibited calcineurin activity. These two calcineurin inhibitors suppressed phagocytosis of fluorescently labeled yeast in a dose-dependent manner. Although it inhib~ted phagocytosis, cyclosporin A had an insignificant effect on the macropinocytosis of the fluid-phase marker fluorescein isothiocyanatedextran. Furthermore, trifluoperazine, a calmodulin antagonist that indirectly inhibits calcinewin, also suppressed phagocytosis in a dosedependent fashion and induced the formation of giant intracellular vacuoles Fluorescence microscopy of cyclosporin A-treated (for 30 min.) cells stained with rhodamine-phalloidin had cytoplasmic chunks of F-actin that were not present in control cells, while cells treated with FK506 and trifluoperazine (also for 30 min.), displayed less cortical but more cytoplasmic F-actin staining than normal cells. Typically, drug-treated cells were smaller and rounder than untreated cells. Our data suggest calcineurin may play a role in D. discoideum phagocytosis, either through the dephosphorylation of actinregulating proteins or other cytoskeletal proteins such as the heavy chain subunit of nonmuscle myosin I1 since dephosphorylation of the latter promotes filament assembly

A role for calcineurin in Dictyostelium discoideum phagocytosis

The Ca2+/calmodul1n-dependent protein phosphatase calcinewin is involved in the development of the cellular slime mold Dictyostelium discoideum. Because of its interactions with Ca2+, which appear to influence D. discoideum phagocytosis (Yuan and Chia, 1999, Mol. Biol. Cell 10, 220a), we undertook studies to test whether calcineurin also plays a role in Dictyostelium phagocytosis. The immunosuppressants cyclosporin A and FK506, through the formation of cyclosporin A-cyclophilin A and FK506- FK506-binding protein complexes, respectively, inhibited calcineurin activity. These two calcineurin inhibitors suppressed phagocytosis of fluorescently labeled yeast in a dose-dependent manner. Although it inhib~ted phagocytosis, cyclosporin A had an insignificant effect on the macropinocytosis of the fluid-phase marker fluorescein isothiocyanatedextran. Furthermore, trifluoperazine, a calmodulin antagonist that indirectly inhibits calcinewin, also suppressed phagocytosis in a dosedependent fashion and induced the formation of giant intracellular vacuoles Fluorescence microscopy of cyclosporin A-treated (for 30 min.) cells stained with rhodamine-phalloidin had cytoplasmic chunks of F-actin that were not present in control cells, while cells treated with FK506 and trifluoperazine (also for 30 min.), displayed less cortical but more cytoplasmic F-actin staining than normal cells. Typically, drug-treated cells were smaller and rounder than untreated cells. Our data suggest calcineurin may play a role in D. discoideum phagocytosis, either through the dephosphorylation of actinregulating proteins or other cytoskeletal proteins such as the heavy chain subunit of nonmuscle myosin I1 since dephosphorylation of the latter promotes filament assembly

Integrity of the actin cytoskeleton required for both phagocytosis and macropinocytosis in \u3ci\u3eDictyostelium discoideum\u3c/i\u3e

Filamentous (F-) actin is enriched in cellular extensions, such as phagocytic cups and macropioocytic crowns, of Dlctyostelium discoideum amebae. Previous studies of actin-disrupting agents that implicated the involvement of the actin cytoskeleton in Dictyostelium phagocytosis and pinocytosis, however, have yielded conflicting results. We show that the integrity of the actin cytoskeleton is required for both phagocytosis and macropinocytosis in D. discoideum with latrunculin A (IatA), which binds to monomeric actin, and cytochalasin A (cytA), which caps the plus end of actin filaments. Using rhodamine-phalloidin to visualize F-actin, cells treated for 30 min. with 1 to 4 pM of latA displayed an increasing dissolution of the cortical actin cytoskeleton that was accompanied by the appearance of numerous cytoplasmic dots of F-actin. In parallel, phagocytosis of fluorescently labeled yeast and macropinocytosis of the fluid-phase marker fluorescein isothiocyanate-dextran both were inhibited in a dose-dependent manner. Cells were nearly devoid of F-actin at latA concentrations greater than 5pM whereas the uniform distribution of monomeric actin appeared unaffected. Cells gradually recovered their intact actin cytoskeleton and concomitantly, their phagocytic and macropinocytic activities when latA was removed by washing. To achieve 50% inhibition of phagocytosis or macropinocytosis, five-fold more cytA than latA was required. Unlike latA-treated cells, cytAtreated cells stained with rhodamine phalloidin retained an actin cytoskeleton even at high concentrations (\u3e25 μM), but were smaller and rounder than untreated cells. The cortical F-actin, however, appeared irregular, and almost discontinuous, which made the cells seem stiff and rigid in comparison to normal cells that looked more fluid and plastic. The distinctive alterations in the cytoskeletal patterns reflected the specific modes of action of the drugs on the actin network that was vital for both phagocytosis and macropinocytosis

Cellular Ability to Sense Spatial Gradients in the Presence of Multiple Competitive Ligands

Many eukaryotic and prokaryotic cells can exhibit remarkable sensing ability under small gradient of chemical compound. In this study, we approach this phenomenon by considering the contribution of multiple ligands to the chemical kinetics within Michaelis-Menten model. This work was inspired by the recent theoretical findings from Bo Hu et al. [Phys. Rev. Lett. 105, 048104 (2010)], our treatment with practical binding energies and chemical potential provides the results which are consistent with experimental observations.Comment: 5 pages, 4 figure