Microcanonical versus canonical analysis of protein folding

The microcanonical analysis is shown to be a powerful tool to characterize the protein folding transition and to neatly distinguish between good and bad folders. An off-lattice model with parameter chosen to represent polymers of these two types is used to illustrate this approach. Both canonical and microcanonical ensembles are employed. The required calculations were performed using parallel tempering Monte Carlo simulations. The most revealing features of the folding transition are related to its first-order-like character, namely, the S-bend pattern in the caloric curve, which gives rise to negative microcanonical specific heats, and the bimodality of the energy distribution function at the transition temperatures. Models for a good folder are shown to be quite robust against perturbations in the interaction potential parameters.     

A reconsideration of acoustic invariance for place of articulation in diffuse stop consonants: evidence from a cross-language study

This study explored the claim that invariant acoustic properties corresponding to phonetic features generalize across languages. Experiment I examined whether the same invariant properties can characterize diffuse stop consonants in Malayalam, French, and English. Results showed that, contrary to theoretical predictions, we could not distinguish labials from dentals, nor could we classify dentals and alveolars together in terms of the same invariant properties. We developed an alternative metric based on the change in the distribution of spectral energy from the burst onset to the onset of voicing. This metric classified over 91% of the stops in Malayalam, French, and English. In experiment II, we investigated whether the invariant properties defined by the metric are used by English-speaking listeners in making phonetic decisions for place of articulation. Prototype CV syllables--[b d] in the context of [i e a o u]--were synthesized. The gross shape of the spectrum was manipulated first at the burst onset, then at the onset of voicing, such that the stimulus configuration had the spectral properties prescribed by our metric for labial and dental consonants, while the formant frequencies and transitions were appropriate to the contrasting place of articulation. Results of identification tests showed that listeners were able to perceive place of articulation as a function of the relative distribution of spectral energy specified by the metric.     

Phase transitions induced by saddle points of vanishing curvature

Based on the study of saddle points of the potential energy landscapes of generic classical many-particle systems, we present a necessary criterion for the occurrence of a thermodynamic phase transition. Remarkably, this criterion imposes conditions on microscopic properties, namely, curvatures at the saddle points of the potential, and links them to the macroscopic phenomenon of a phase transition. We apply our result to two exactly solvable models, corroborating that the criterion derived is not only valid, but also sharp and useful: For both models studied, the criterion excludes the occurrence of a phase transition for all values of the potential energy but the transition energy. This result adds a geometrical ingredient to an established topological condition for the occurrence of a phase transition, thereby providing an answer to the long-standing question of which topology changes in configuration space can induce a phase transition.     

Simple Model Study of Phase Transition Properties of Isolated and Aggregated Protein

We investigate the phase transition properties of isolated and aggregated protein by exhaustive numerical study in the confined conformation space with maximally compact lattice model. The study within the confined conformation space shows some general folding properties. Various sequences show different folding properties: two-state folding, three-state folding and prion-like folding behavior. We find that the aggregated protein holds a more evident transition than isolated one and the transition temperature is generally lower than that in isolated case.     

Surface electroluminescence phenomena correlated with trapping parameters of insulating polymers

Electroluminescence (EL) phenomena are closely linked to the space charge and degradation in insulating polymers, and dominated by the luminescence and trap centers. EL emission has been promising in defining the onset of electrical aging and in the investigation of dissipation mechanisms. Generally, polymeric degradation reveals the increment of the density of luminescence and trap centers, so a fundamental study is proposed to correlate the EL emission of insulating polymers and their trapping parameters. A sensitive photon counting system is constructed to detect the weak EL. The time- and phase-resolved EL characteristics from different polymers (LDPE, PP and PTFE) are investigated with a planar electrode configuration under stepped ac voltage in vacuum. In succession, each sample is charged with exposing to multi-needle corona discharge, and then its surface potential decay is continuously recorded at a constant temperature. Based on the isothermal relaxation current theory, the energy level and density of both electron and hole trap distribution in the surface layer of each polymer is obtained. It is preliminarily concluded that EL phenomena are strongly affected by the trap properties, and for different polymers, its EL intensity is in direct contrast to its surface trap density, and this can be qualitatively explained by the trapping and detrapping sequence of charge carriers in trap centers with different energy level.     

Smoothing potential energy surface of proteins by hybrid coarse grained approach

Coarse-grained(CG) simulations can more efficiently study large conformational changes of biological polymers but usually lose accuracies in the details. Lots of different hybrid models involving multiple different resolutions have been developed to overcome the difficulty. Here we propose a novel effective hybrid CG(hyCG) approach which mixes the fine-grained interaction and its average in CG space to form a more smoothing potential energy surface. The hyCG approximately reproduces the potential of mean force in the CG space, and multiple mixed potentials can be further combined together to form a single effective force field for achieving both high efficiency and high accuracy. We illustrate the hyCG method in Trp-cage and Villin headpiece proteins to exhibit the folding of proteins. The topology of the folding landscape and thus the folding paths are preserved, while the folding is boosted nearly one order of magnitude faster. It indicates that the hyCG approach could be applied as an efficient force field in proteins.     

CN~+离子电子结构和跃迁性质的理论研究

采用多组态参考相互作用方法和AV5Z-DK基组对CN~+离子的两个解离极限C~+(~2P_u)+N(~2D_u)和C~+(~2P_u)+N(~4S_u)下的X~1Σ~+、a~3Π、~1Δ和A~1四个电子态的势能曲线、永久偶极矩和振动能级进行了计算.为保证计算结果的精确性,在计算中考虑了Davidson修正.基于求得的势能曲线,数值求解一维径向薛定谔方程得到了各个电子态的光谱数据,并与实验值和已有的理论值吻合较好.除此之外,对A~1Π→X~1Σ~+和1~1Δ?A1~Π的跃迁性质进行了研究,同时通过跃迁的弗兰克-康登因子及辐射寿命,对CN~+离子激光冷却的可行性进行了分析.     

Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I

We have investigated the folding properties of tryptophan zipper-I molecule which folds into a stable β-hairpin motif in aqueous solution as suggested by nuclear magnetic resonance (NMR) experiments. An all-atom presentation, including hydrogen, was used with an implicit solvent. As a simulation technique, simulated tempering algorithm was used to obtain equilibrium conformations of the molecule at ten distinct temperatures. Our minimum energy configuration obtained from simulated tempering algorithm is a β-hairpin motif with 1.30 Å backbone root-mean-square deviation from the reference PDB structure (1le0.pdb). Several quantities and exhaustive folding free energy landscapes were determined and discussed in order to clarify the folding behavior.     

Diffusive model of protein folding dynamics with Kramers turnover in rate

We study the folding kinetics of a three-helix bundle protein using a coarse polymer model. The folding dynamics can be accurately represented by one-dimensional diffusion along a reaction coordinate selected to capture the transition state. By varying the solvent friction, we show that position-dependent diffusion coefficients are determined by microscopic transitions on a rough energy landscape. A maximum in the folding rate at intermediate friction is explained by "Kramers turnover" in these microscopic dynamics that modulates the rate via the diffusion coefficient; overall folding remains diffusive even close to zero friction. For water friction, we find that the "attempt frequency" (or "speed limit") in a Kramers model of folding is about 2 micros-1, with an activation barrier of about 2kBT, and a folding transition path duration of approximately equal to 100 ns, 2 orders of magnitude less than the folding time of approximately equal to 10 micros.     

Syntheses and optical properties of triphenylene-containing conjugated polymers

In this paper, we report the detailed synthesis and optical properties of three new conjugated polymers containing triphenylene units in the backbone. Polymer PTPT exhibits strong folding propensity and forms foldamers in both polar and nonpolar solvents. PTPA, with two long alkyl chains attached to the bridging phenyl ring, exhibits mainly as interchain aggregates in “poor” solvents (DMSO and acetonitrile), but adopts a folding conformation in solvent mixtures with a high poor solvent content. PTPV, on the other hand, adopts a random nonfolding conformation in both polar and nonpolar solvents. The low folding propensity of PTPV is likely due to the added geometrical flexibility of the vinyl bonds. Among the three polymers, PTPV is most fluorescent with a fluorescence quantum yield as high as 0.87, suggesting its potential applications as light-emitting materials or fluorescence-based sensors. PTPT, on the other hand, with its strong folding property, may find applications as efficient charge-transporting materials.     

Solitons in One‐Dimensional Lattices with a Flat Band

We investigate the spectral properties of a quasi‐one‐dimensional lattice in two possible dimerisation configurations. Both configurations are characterised by the same lattice topology and the identical spectra containing a flat band at zero energy. We find that, one of the dimerised configuration has similar symmetry to a one‐dimensional chain proposed by Su‐Schrieffer‐Heeger for studying solitons in conjugated polymers. Whereas, the other dimerised configuration only shows non‐trivial topological properties in the presence of chiral‐symmetry breaking adiabatic pumping.     

Analytical potential energy function and spectroscopy parameters for B~1Π state of KH

Multi-reference configuration interaction is used to produce potential energy curves(PECs) for the excited B1Π state of KH molecule.To investigate the correlation effect of core-valence electrons,five schemes are employed which include the different correlated electrons and different active spaces.The PECs are fitted into analytical potential energy functions(APEFs).The spectroscopic parameters,ro-vibrational levels,and transition frequencies are determined based on the APEFs and compared with available experimental and theoretical data.The molecular properties for B1Π obtained in this letter,which are better than those available in literature,can be reproduced with calculations using the suitable correlated electrons and active space of orbitals.     

Evidence of glass transition in thin films of maleic anhydride derivatives: Effect of the surfactant coadsorption

The glass transition temperature of poly (maleic anhydride-alt-1-octadecen) and poly (styreneco-maleic anhydride) cumene-terminated thin films has been measured by mechanical relaxation of Langmuir films of these polymers. The dynamical properties show glass-like features (non-Arrhenius relaxation times and non-Debye mechanical response) interpreted by the coupling model. The glass transition temperature values determined by a mechanical relaxation experiment (step-compression) agree very well with those obtained by surface potential measurements. It is found that the glass transition temperature values in thin films decrease by about 100K as compared with those corresponding to the bulk polymers. The coadsorption of the water-insoluble surfactant DODAB decreases the glass transition temperature.     

Buckling instabilities of one-layered growing tissues

Growth and folding in one-layered model tissue sheets are studied in a stochastic, lattice-free single cell model which considers the discrete cellular structure of the tissue, and in a coarse grained analytical approach. The polarity of the one-layered tissue is considered by a bending term. Cell division gives rise to a locally increasing metric. An exponential and a power-law growth regime are identified. In both regimes, folding occurs as soon as the bending contribution becomes too small to compensate the destabilizing effect of the cell proliferation. The potential biological relevance is discussed.     

Interface water-induced hydrophobic carbon chain unfolding in water

The folding and unfolding of the carbon chain, which is the basic constitutional unit of polymers,are important to the performance of the material. However, it is difficult to regulate conformational transition of the carbon chain, especially in an aqueous environment. In this paper, we propose a strategy to regulate the conformational transition of the carbon chain in water based on the all-atom molecular dynamics simulations. It is shown that the unfolded carbon chain will spontaneously collapse into the folded state, while the folded carbon chain will unfold with an external electric field. The regulation ability of the electric field is attributed to the electric field-induced redistribution of interface water molecules near the carbon chain. The demonstrated method of regulating conformational transition of the carbon chain in water in this study provides an insight into regulating hydrophobic molecules in water, and has great potential in drug molecule design and new polymer material development.     

Coulomb repulsion-induced hyperbolic pairing as a mechanism of high-T c superconductivity

The hyperbolic metric of the dispersion law (the effective mass tensor components of carriers are opposite in sign) in the vicinity of the Fermi contour in high-T _c superconducting cuprates in the case of repulsive interaction gives rise to a superconducting state characterized by the condensate of pairs with a large total momentum (hyperbolic pairing). The gain in the energy of the superconducting state over the normal state is due to the fact that a change in the kinetic energy of pairs (because of the negative light component of the effective mass) dominates over the change in the potential energy (corresponding to energy loss). The shift of the chemical potential upon the transition to the superconducting phase is substantial in this case. With increasing repulsive interaction, the superconducting gap δ_K increases and the resulting gain in energy changes to an energy loss at a certain critical value of the repulsive potential. The low temperature T _c of the superconducting transition and the large value of δ _K in this region of potential values are the reasons for the high value of the 2δ_K/T _c ratio and for the developed quantum fluctuations that are observed in underdoped cuprate superconductors.     

Global monopole in general relativity

We consider the gravitational properties of a global monopole on the basis of the simplest Higgs scalar triplet model in general relativity. We begin with establishing some common features of hedgehog-type solutions with a regular center, independent of the choice of the symmetry-breaking potential. There are six types of qualitative behaviors of the solutions; we show, in particular, that the metric can contain at most one simple horizon. For the standard Mexican hat potential, the previously known properties of the solutions are confirmed and some new results are obtained. Thus, we show analytically that solutions with the monotonically growing Higgs field and finite energy in the static region exist only in the interval 1 < λ < 3, where λ is the squared energy of spontaneous symmetry breaking in Planck units. The cosmological properties of these globally regular solutions apparently favor the idea that the standard Big Bang might be replaced with a nonsingular static core and a horizon appearing as a result of some symmetry-breaking phase transition at the Planck energy scale. In addition to the monotonic solutions, we present and analyze a sequence of families of new solutions with the oscillating Higgs field. These families are parametrized by n, the number of knots of the Higgs field, and exist for λ < γ_n=6/[(2n + 1)(n + 2)]; all such solutions possess a horizon and a singularity beyond it.     

软凝聚态物质物理学

软物质是指其某种物理性质在小的外力作用下能产生很大变化的凝聚态物,典型的例子包括液晶、高分子体系、胶体、微乳液等。软物质的结构和性质主要不是由内能,而是由熵来决定,较通俗地介绍了软物质的概念,仔细分析了熵在软物质中所起的作用,同时详细介绍了聚合物体系、胶体及生物膜等几种典型的软物质,通过硫化橡胶和无管虹吸等十分有趣的例子。说明了聚合物对流变性质的影响;通过分析硬球胶体的相变及相分离等行为说明了熵力的概念;仔细分仔了电稳定胶体的相互作用,并介绍了DLVO理论以及近年来发现的对这一理论的偏离,特别是约束条件下同号带电胶球的长程吸引相互作用及其对此现象的一些解释;对生物膜也作了初步介绍。人们对软物质的研究和理解目前还处于一个非常原始的阶段,深入研究和理解软物质的各种性质必将促进人类对自然和人类自身的认识。