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This paper presents the results of dynamic behavior modeling of phase states (solid and liquid) of water clusters ((H2O)8, (H2O)10, and (H2O)12) by molecular dynamics method. The initial configurations of the clusters were cube for octamer, pentagonal prism for decamer, and fused-cube structure for dodecamer. The different analytical interaction potentials (TIPnP (n = 3, 4), SPC, and SPC/E) were applied to the phase dynamics of water octamer to choose the most appropriate potential for the study. The dynamic criteria based on the molecule’s potential energy distribution were applied for identification of solid and liquid phases of decamer and dodecamer. The most probable conformers of decamer and dodecamer in different phases were obtained.

Intrinsically disordered regions (IDRs) are often fast-evolving protein domains of low sequence complexity that can drive phase transitions and are commonly found in many proteins associated with neurodegenerative diseases, including the RNA processing factor TDP43. Yet, how phase separation contributes to the physiological functions of TDP43 in cells remains enigmatic. Here, we combine systematic mutagenesis guided by evolutionary sequence analysis with a live-cell reporter assay of TDP43 phase dynamics to identify regularly-spaced hydrophobic motifs separated by flexible, hydrophilic segments in the IDR as a key determinant of TDP43 phase properties. This heuristic framework allows customization of the material properties of TDP43 condensates to determine effects on splicing function. Remarkably, even a mutant that fails to phase-separate at physiological concentrations can still efficiently mediate the splicing of a quantitative, single-cell splicing reporter and endogenous targets. This suggests that the ability of TDP43 to phase-separate is not essential for its splicing function., TDP43 regulates RNA processing and undergoes liquid-liquid phase separation. Here, the authors combine bioinformatic analysis and quantitative measurements of phase properties in living cells to uncover the rules that link the amino acid sequence of TDP43 with its phase properties and find that unexpectedly, mutants of TDP43 that are deficient in phase separation can still function to mediate splicing.

In addition to the nucleophile and solvent, the leaving group has a significant influence on SN2 nucleophilic substitution reactions. Its role is frequently discussed with respect to reactivity, but its influence on the reaction dynamics remains unclear. Here, we uncover the influence of the leaving group on the gas-phase dynamics of SN2 reactions in a combined approach of crossed-beam imaging and dynamics simulations. We have studied the reaction F(-) + CH3Cl and compared it to F(-) + CH3I. For the two leaving groups, Cl and I, we find very similar structures and energetics, but the dynamics show qualitatively different features. Simple scaling of the leaving group mass does not explain these differences. Instead, the relevant impact parameters for the reaction mechanisms are found to be crucial and the differences are attributed to the relative orientation of the approaching reactants. This effect occurs on short timescales and may also prevail in solution-phase conditions.

The addition of trace molecules into membranes can significantly alter the morphology of the co-existing liquid phases and lipid phase transition temperature. Membrane additives may affect lipid phase dynamics through preferentially partitioning to the boundary between lipid phases or preferentially mixing into one lipid phase. The characteristic differences between these mechanisms are demonstrated here in a minimalistic nearest neighbor model to provide a framework for how slight changes to membrane composition may affect lipid-phase-dependent processes, such as lipid-raft formation, immunological signaling, and molecular sorting preceding endocytosis with coexisting liquid phases. Within the low mole fractions explored here (≤3 mol%), increasing the additive concentration linearly changed the phase miscibility temperature. Rotationally asymmetric Janus particles reduced the miscibility transition temperature for all fractions and degree of phase polarization. Rotationally symmetric additives, however, either increased or decreased the phase miscibility temperature depending on the phase preference of the additive. While most experimental molecules may contain aspects of both of these idealized additives, this model provides a broad framework to quantify the effects of membrane additives in regard to lipid phase preference, lipid-raft association, and contribution to lipid phase-dependent molecular sorting. Electronic supplementary material The online version of this article (doi:10.1007/s00249-015-1017-x) contains supplementary material, which is available to authorized users.

Both autoregulation and CO(2) reactivity are known to have significant effects on cerebral blood flow and thus on the transport of oxygen through the vasculature. In this paper, a previous model of the autoregulation of blood flow in the cerebral vasculature is expanded to include the dynamic behavior of oxygen transport through binding with hemoglobin. The model is used to predict the transfer functions for both oxyhemoglobin and deoxyhemoglobin in response to fluctuations in arterial blood pressure and arterial CO(2) concentration. It is shown that only six additional nondimensional groups are required in addition to the five that were previously found to characterize the cerebral blood flow response. A resonant frequency in the pressure-oxyhemoglobin transfer function is found to occur in the region of 0.1 Hz, which is a frequency of considerable physiological interest. The model predictions are compared with results from the published literature of phase angle at this frequency, showing that the effects of changes in breathing rate can significantly alter the inferred phase dynamics between blood pressure and hemoglobin. The question of whether dynamic cerebral autoregulation is affected under conditions of stenosis or stroke is then examined.

The activities of lectins and peroxidase and lignin content were studied in the perilesional area of leaves in two tobacco species (Nicotiana tabacumL., cultivar Samsun NN, and N. glutinosa L.) inoculated with tobacco mosaic virus. The development of hypersensitivity response proved to be accompanied by a complex spatial and temporal distribution of lectin activity. The area 5–9 mm away from the lesion center was characterized by the highest activity of loosely bound membrane lectins eluted with 0.05% Triton X-100. In the fraction of tightly bound membrane lectins (eluted with 0.5% detergent), lectin activity decreased during the first two days but increased on day 4 after inoculation. The activity of loosely bound membrane lectins increased in the leaf areas distant from the lesion. Two-phase dynamics in the interlesional area were also observed for lectin activity in the tightly bound membrane fraction (decrease on day 2 days and increase on day 4 after inoculation) and for peroxidase activity (increase on day 2 days and decrease on day 4). The relationship between the dynamics and spatial distribution of lectins in the perilesional area and the possible involvement of these proteins in pathogen-induced changes in photosynthesis are discussed.

High temperature Mossbauer spectroscopy has been used for studying “in situ” the phase dynamics of the silicon rich part of the binary Fe-Si system. In particular the rate and mechanism of the transformation of the so-called zeta-alpha phase of iron disilicide to the zeta-beta phase is of special interest, since there still remains uncertainty about the stability and the structure of the phase in this system which influence material properties such as compressive strength and disintegration. In the present work the phase transition from the zeta-alpha phase to the zeta-beta phase is followed by a time sequence of Mossbauer spectra recorded every three hours at a fixed temperature around 800 K. The exponential precipitation rate is analysed and the exponent calculated. Samples with differing degree of impurities have been studied and the effect of aluminium impurities on the rate of the transition will be discussed. The Debye temperature of the two phases was determined from series of Mossbauer spectra recorded at temperatures between 300 and 800 K.

The spin-spin relaxation time measured from the line width (T 2*) is used to study bonded phase dynamics of two liquid crystal materials in the solid state as a function of temperature. The motion of these two bonded phases is much more restricted than either C-18 or butyl phenyl bonded to the same substrate. Plots ofT 2* vs. 1/T indicate a structural transition of the bonded phase moiety for the two liquid crystal materials but no such change is seen for either C-18 or butyl phenyl over the same temperature range (243–353 K), suggesting a higher degree of association between adjacent bonded moieties for the two liquid crystal materials in comparison to the other two phases. The conclusions from solid-state NMR data coincide with results obtained in earlier chromatographic studies.

We present studies of phase dynamics of the silicon rich part of the Fe−Si system performed with Mossbauer spectroscopy. Standard spectra are obtained in very pure samples and these are applied to the studies of commercial 75& ferrosilicon. We find that the semistable high temperature alpha phase, known for considerable concentration of vacancies, needs multiple quadrupole doublets to fit the data. Finally it is shown how the Mossbauer effect can be applied to quality control in ferrosilicon production.

Various laser-based deposition methods for preparation of silicon films have been reviewed briefly with emphasis on laser chemical vapor deposition (CVD). The main body of this paper is concerned with CO2laser CVD of silane. This is interesting because the observed dependence of deposition rates on laser wavelengths indicates that gas-phase reactions are involved in deposition processes and therefore we can apply a powerful new diagnostic means, coherent anti-Stokes Raman spectroscopy (CARS), to examine gas-phase dynamics. From N2CARS thermometry the CO2laser beams were found to raise the temperature of the gas containing silane, when they were tuned to absorption lines of SiH4. Silane CARS spectra were characterized by a complicated profile with double peaks. We interpreted the shape of the spectra as arising from excitation of rotational levels following gas-phase reactions. Applying this interpretation, we can judge how SiH4molecules are disturbed differently according to CO2laser wavelengths and a distance from a substrate.