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.

Formation of ordered microphase-separated pattern during spin coating of ABC triblock copolymer

In this paper, the authors have systematically studied the microphase separation and crystallization during spin coating of an ABC triblock copolymer, polystyrene-b-poly(2-vinylpyridine)-b-poly(ethylene oxide) (PS-b-P2VP-b-PEO). The microphase separation of PS-b-P2VP-b-PEO and the crystallization of PEO blocks can be modulated by the types of the solvent and the substrate, the spinning speed, and the copolymer concentration. Ordered microphase-separated pattern, where PEO and P2VP blocks adsorbed to the substrate and PS blocks protrusions formed hexagonal dots above the P2VP domains, can only be obtained when PS-b-P2VP-b-PEO is dissolved in N,N-dimethylformamide and the films are spin coated onto the polar substrate, silicon wafers or mica. The mechanism of the formation of regular pattern by microphase separation is found to be mainly related to the inducement of the substrate (middle block P2VP wetting the polar substrate), the quick vanishment of the solvent during the early stage of the spin coating, and the slow evaporation of the remaining solvent during the subsequent stage. On the other hand, the probability of the crystallization of PEO blocks during spin coating decreases with the reduced film thickness. When the film thickness reaches a certain value (3.0 nm), the extensive crystallization of PEO is effectively prohibited and ordered microphase-separated pattern over large areas can be routinely prepared.

Pattern formation in a confined polymer film induced by a temperature gradient

We have studied a morphological instability of a double layer comprising the polymer film and air gap confined between the two plates set to different temperatures. The temperature gradient across the double layer causes the breakup of the polymer film into well-defined columnar, striped or spiral structures spanning the two plates. The pattern formation mechanisms have been discussed. The formed patterns can be transferred to produce PDMS stamp, a key element of soft lithography for future microfabrication.

Ordered pattern formation from dewetting of polymer thin film with surface disturbance by capillary force lithography

The dewetting process of thin polystyrene (PS) film with built-in ordered disturbance by capillary force lithography (CFL) has. been investigated in situ by AFM. Two different phenomena are observed depending on the excess surface energy (DeltaF(gamma)) of the system. When DeltaF(gamma) is less than a certain critical value (i.e., the disturbance amplitude is under a critical value), the PS film would be flattened and become stable finally by heating above T-g. While, if the size of the disturbance amplitude is larger than the critical value, ordered PS liquid droplets form by further dewetting. The pattern formation mechanisms and influencing factors have been discussed in detail.

NMR and pattern recognition studies on the acute biochemical effects of Lu(NO3)(3)

Pattern recognition methods were applied to the analysis of 600 MHz H-1 NMR spectra of urine from rats dosed with compounds that induced organ-specific damage in the liver and kidney. Male Wistar rats were separated into groups (n=4) and each was treated with one of following compounds: HgCl2, CCl4, Lu(NO3)(3) and Changle (a kind of rare earth complex mixed with La, Ce, Pr and Nd). Urine samples from the rats dosed with HgCl2, CCl4 and Lu(NO3)(3) were collected over a 24 h time course and the samples from the rats administrated with Changle were gained after 3 months. These samples were measured by 600 MHz NMR spectroscopy. Each spectrum was data-processed to provide 223 intensity-related descriptors of spectra. Urine spectral data corresponding to the time intervals, 0-8 h (HgCl2 and CCl4), 4-8 (Lu(NO3)(3)) h and 90 d (Changle) were analyzed using principal component analysis (PCA). Successful classification of the toxicity and biochemical effects of Lu(NO3)(3) was achieved.

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.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

Discrimination of herbal medicines by molecular spectroscopy and chemical pattern recognition

The molecular spectroscopy (including near infrared diffuse reflection spectroscopy, Raman spectroscopy and infrared spectroscopy) with OPUS/Ident software was applied to clustering ginsengs according to species and processing methods. The results demonstrate that molecular spectroscopic analysis could provide a rapid, nondestructive and reliable method for identification of Chinese traditional medicine. It's found that the result of Raman spectroscopic analysis was the best one among these three methods. Comparing with traditional methods, which are laborious and time consuming, the molecular spectroscopic analysis is more effective.

How to form regular polymer microstructures by surface-pattern-directed dewetting

The substrates with regular patterns of self-assembly monolayers (SAMs) produced by microcontact printing with octadecyltrichlorosilane (OTS) was employed to direct thin polystyrene dewetting to fabricate ordered micrometer scale pattern. The pattern sizes and pattern fashion can be manipulated by controlling the experimental parameters. The pattern formation mechanisms have been discussed. The dewetting pattern can be transferred to form PDMS stamp for future microfabrication process.

Patterning thin polymer films by surface-directed dewetting and pattern transfer

The pattern evolution processes of thin polystyrene (PS) film on chemically patterned substrates during dewetting have been investigated experimentally. The substrates have patterns of self-assembly monolayers produced by microcontact printing with octadecyltrichlorosilane. Optical microscopy and atomic force microscopy images reveal that ordered micrometer scale pattern can be created by surface direct dewetting. Various pattern sizes and pattern complexities can be achieved by controlling the experimental parameters. The dewetting pattern has been transferred to form PDMS stamp for soft lithography.

Pattern formation in polymer films under the mask

This paper presents a straightforward method for patterning thin films of polymers, i.e. a prepatterned mask is used to induce self-assembly of polymers and the resulting pattern is the same as the lateral structures in the mask on a submicrometre length scale, The patterns can be formed at above T-g + 30 degreesC in a short time and the external electric field is not crucial. Electrostatic force is assumed to be the driving force for the pattern transfer. Viscous fingering and novel stress-relief lateral morphology induced under the featureless mask are also observed and the formation mechanisms are discussed.

Formation of regular hole pattern in polymer films

Ordered macroporous materials recently have attracted much attention. A method that utilizes the condensation of monodisperse water droplets on a polymer solution is proposed for the preparation of honeycomb microporous films. Our results show that it is a general method that can be used for patterning a wide range of polymers. The presence of water vapor and polymer is necessary for the formation of regular holes in films. The formation of hexagonal packing instead of other kinds of packing takes place because the hexagonal packing has the lowest free energy. The formation mechanisms of regular hole pattern and imperfections in the hexagonal packing are proposed.

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.

Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We found that the first passage-time (FPT) distribution undergoes a dynamic transition at a temperature below which the FPT distribution develops a power-law tail, a signature of the intermittent nonexponential kinetic phenomena for the folding dynamics. Possible applications to single-molecule dynamics experiments are discussed.