Robustness and dissipation of mitogen-activated protein kinases signal transduction network: Underlying funneled landscape against stochastic fluctuations

We uncovered the underlying energy landscape of the mitogen-activated protein kinases signal transduction cellular network by exploring the statistical natures of the Brownian dynamical trajectories. We introduce a dimensionless quantity: The robustness ratio of energy gap versus local roughness to measure the global topography of the underlying landscape. A high robustness ratio implies funneled landscape. The landscape is quite robust against environmental fluctuations and variants of the intrinsic chemical reaction rates.

Exploring the Origin of Power Law Distribution in Single-Molecule Conformation Dynamics: Energy Landscape Perspectives

We explored the origin of power law distribution observed in single-molecule conformational dynamics experiments. By establishing a kinetic master equation approach to study statistically the microscopic state dynamics, we show that the underlying landscape with exponentially distributed density of states leads to power law distribution of kinetics. The exponential density of states emerges when the system becomes glassy and landscape becomes rough with significant trapping.

Phase transformation and photoluminescence properties of nanocrystalline ZrO2 powders prepared via the Pechini-type sol-gel process

Nanocrystalline ZrO2 fine powders were prepared via the Pechini-type sol-gel process followed by annealing from 500 to 1000 degrees C. The obtained ZrO2 samples were characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), electron paramagnetic resonance (EPR), and photoluminescence spectra (PL), respectively. The phase transition process from tetragonal (T) to monoclinic (M) was observed for the nanocrystalline ZrO2 powders in the annealing process, accompanied by the change of their photoluminescence properties. The 500 degrees C annealed ZrO2, powder with tetragonal structure shows an intense whitish blue emission (lambda(max) = 425 nm) with a wide range of excitation (230-400 nm). This emission decreased in intensity after being annealed at 600 degrees C (T + M-ZrO2) and disappeared at 700 (T + M-ZrO2), 800 (T + M-ZrO2), and 900 degrees C (M-ZrO2). After further annealing at 1000 degrees C (M-ZrO2), a strong blue-green emission appeared again (lambda(max) = 470 nm).

Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives

Three-protein circadian oscillations in cyanobacteria sustain for weeks. To understand how cellular oscillations function robustly in stochastic fluctuating environments, we used a stochastic model to uncover two natures of circadian oscillation: the potential landscape related to steady-state probability distribution of protein concentrations; and the corresponding flux related to speed of concentration changes which drive the oscillations. The barrier height of escaping from the oscillation attractor on the landscape provides a quantitative measure of the robustness and coherence for oscillations against intrinsic and external fluctuations. The difference between the locations of the zero total driving force and the extremal of the potential provides a possible experimental probe and quantification of the force from curl flux. These results, correlated with experiments, can help in the design of robust oscillatory networks.

Coordination-Induced Formation of One-Dimensional Nanostructures of Europium Benzene-1,3,5-tricarboxylate and Its Solid-State Thermal Transformation

Novel one-dimensional europium benzene-1,3,5-tricarboxylate compressed nanorods have been synthesized oil it large scale through direct precipitation in solution phase under moderate conditions without the assistance of any surfactant, catalyst, or template. The obtained nanorods have widths of about 50-100 not, thicknesses of 10-20 nm, and lengths ranging from a few hundred nanometers to several micrometers. X-ray powder diffraction. elemental analysis, Fourier transform infrared Studies, and thermogravimetric and differential thermal analysis show that the nanorods have the structural formula of Eu(1,3,5-BTC)center dot 6H(2)O. Upon UV excitation, these nanorods exhibit a highly efficient luminescence. which comes from the Eu3+ ions. Moreover, Eu2O3 nanorods Could also be obtained via a thermal decomposition method using the corresponding complex as a precursor. This synthetic route is promising for the preparation of other one-dimensional crystalline nanomaterials because of its simplicity and the low cost of the starting reagents.

Facile transformation of hydrophilic cellulose into superhydrophobic cellulose

Superhydrophobic cellulose-based materials coupled with transparent, stable and nanoscale polymethylsiloxane coating have been successfully achieved by a simple process via chemical vapor deposition, followed by hydrolyzation and polymerization.

Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Transformation from ordered islands to holes in phase-separating P2VP/PS blend films by adding triton X-100

Our previous investigation showed that the ordered hexagonal island pattern in the phase-separating polymeric blend films of polystyrene and poly(2-vinylpyridine) (PS/P2VP) formed due to the convection effect by proper control of PS molecular weight, solvent evaporation rate, and the weight ratio of PS to P2VP. In this paper, we further illustrate that, by adding a proper amount of the surfactant Triton X-100 to the PS/P2VP toluene solution, the ordered hexagonal island pattern can be transformed to the ordered honeycomb pattern. The effects of the amount of Triton X-100 on the surface morphology evolution and the pattern transformation are discussed in terms of the collapse of Triton X-100, phase separation between Triton X-100/P2VP and PS, the interfacial interaction between Triton X-100/P2VP and the mica substrate, and the Benard-Marangoni convection.

The combined catalytic action of solid acids with nickel for the transformation of polypropylene into carbon nanotubes by pyrolysis

The effects of both organically modified montmorillonite (OMMT) and Ni2O3 on the carbonization of polypropylene (PP) during pyrolysis were investigated. The results from TEM and Raman spectroscopy showed that the carbonized products of PP were mainly multiwalled carbon nanotubes (MWNTs). Surprisingly, a combination of OMMT and Ni2O3 led to high-yield formation of MWNTs. X-ray powder diffraction (XRD) and GC-MS were used to investigate the mechanism of this combination for the high-yield formation of MWNTs from PP. Bronsted acid sites were created in degraded OMMT layers by thermal decomposition of the modifiers. The resultant carbenium ions play an important role in the carbonization of PP and the formation of MWNTs. The degradation of PP was induced by the presence of carbenium ions to form predominantly products with lower carbon numbers that could be easily catalyzed by the nickel catalyst for the growth of MWNTs. Furthermore, carbenium ions are active intermediates that promote the growth of MWNTs from the degradation products with higher carbon numbers through hydride-transfer reactions. The XRD measurements showed that Ni2O3 was reduced into metallic nickel (Ni) in situ to afford the active sites for the growth of MWNTs.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Funneled landscape leads to robustness of cellular networks: MAPK signal transduction

We uncover the underlying potential energy landscape for a cellular network. We find that the potential energy landscape of the mitogen-activated protein-kinase signal transduction network is funneled toward the global minimum. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. Funneled landscape is a realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.

Multiple morphologies and their transformation of a polystyrene-block-poly(4-vinylpyridine) block copolymer

We report the multiple morphologies and their transformation of polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) in low-alkanol solvents. In order to improve the solubility of polystyrene block in alcohol solvents, the solution of block copolymer sample was treated at a higher temperature, and then the influence of rate of decreasing temperature on multiple morphologies (including spheres, rods, vesicles, porous vesicles, large compound vesicles, and large compound micelles) was observed. The transformation of spheres to rods, to tyre-shaped large compound micelles, and to sphere-shaped large compound micelles was also realized. The formation mechanisms of the multiple morphologies and their transformation are discussed briefly.