Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes

Residue types at the interface of protein-protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.

Fast and slow climate responses to CO2 and solar forcing: A linear multivariate regression model characterizing transient climate change

Climate change in response to a change in external forcing can be understood in terms of fast response to the imposed forcing and slow feedback associated with surface temperature change. Previous studies have investigated the characteristics of fast response and slow feedback for different forcing agents. Here we examine to what extent that fast response and slow feedback derived from time-mean results of climate model simulations can be used to infer total climate change. To achieve this goal, we develop a multivariate regression model of climate change, in which the change in a climate variable is represented by a linear combination of its sensitivity to CO2 forcing, solar forcing, and change in global mean surface temperature. We derive the parameters of the regression model using time-mean results from a set of HadCM3L climate model step-forcing simulations, and then use the regression model to emulate HadCM3L-simulated transient climate change. Our results show that the regression model emulates well HadCM3L-simulated temporal evolution and spatial distribution of climate change, including surface temperature, precipitation, runoff, soil moisture, cloudiness, and radiative fluxes under transient CO2 and/or solar forcing scenarios. Our findings suggest that temporal and spatial patterns of total change for the climate variables considered here can be represented well by the sum of fast response and slow feedback. Furthermore, by using a simple 1-D heat-diffusion climate model, we show that the temporal and spatial characteristics of climate change under transient forcing scenarios can be emulated well using information from step-forcing simulations alone.

Triplet excited electronic state switching induced by hydrogen bonding: A transient absorption spectroscopy and time-dependent DFT study

The solvent plays a decisive role in the photochemistry and photophysics of aromatic ketones. Xanthone (XT) is one such aromatic ketone and its triplet-triplet (T-T) absorption spectra show intriguing solvatochromic behavior. Also, the reactivity of XT towards H-atom abstraction shows an unprecedented decrease in protic solvents relative to aprotic solvents. Therefore, a comprehensive solvatochromic analysis of the triplet-triplet absorption spectra of XT was carried out in conjunction with time dependent density functional theory using the ad hoc explicit solvent model approach. A detailed solvatochromic analysis of the T-T absorption bands of XT suggests that the hydrogen bonding interactions are different in the corresponding triplet excited states. Furthermore, the contributions of non-specific and hydrogen bonding interactions towards differential solvation of the triplet states in protic solvents were found to be of equal magnitude. The frontier molecular orbital and electron density difference analysis of the T-1 and T-2 states of XT indicates that the charge redistribution in these states leads to intermolecular hydrogen bond strengthening and weakening, respectively, relative to the S-0 state. This is further supported by the vertical excitation energy calculations of the XT-methanol supra-molecular complex. The intermolecular hydrogen bonding potential energy curves obtained for this complex in the S-0, T-1, and T-2 states support the model. In summary, we propose that the different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states of XT result in a decreasing role of the n pi* triplet state, and are thus responsible for its reduced reactivity towards H-atom abstraction in protic solvents. (C) 2016 AIP Publishing LLC.

Transient potassium channels augment degeneracy in hippocampal active dendritic spectral tuning

Hippocampal pyramidal neurons express an intraneuronal map of spectral tuning mediated by hyperpolarization-activated cyclic-nucleotide-gated nonspecific-cation channels. Modeling studies have predicted a critical regulatory role for A-type potassium (KA) channels towards augmenting functional robustness of this map. To test this, we performed patch-clamp recordings from soma and dendrites of rat hippocampal pyramidal neurons, and measured spectral tuning before and after blocking KA channels using two structurally distinct pharmacological agents. Consistent with computational predictions, we found that blocking KA channels resulted in a significant reduction in resonance frequency and significant increases in input resistance, impedance amplitude and action-potential firing frequency across the somato-apical trunk. Furthermore, across all measured locations, blocking KA channels enhanced temporal summation of postsynaptic potentials and critically altered the impedance phase profile, resulting in a significant reduction in total inductive phase. Finally, pair-wise correlations between intraneuronal percentage changes (after blocking KA channels) in different measurements were mostly weak, suggesting differential regulation of different physiological properties by KA channels. Our results unveil a pivotal role for fast transient channels in regulating theta-frequency spectral tuning and intrinsic phase response, and suggest that degeneracy with reference to several coexisting functional maps is mediated by cross-channel interactions across the active dendritic arbor.

Numerical Simulation of Transient Thermal Field and Residual Stress in Laser Melting Process

以激光熔凝表面强韧化处理为背景,应用空间弹塑性有限单元和高精度数值算法同时考虑材料组织性能的变化模拟工件的温度场及残余应力,研究激光熔凝加工中瞬时温度场及残余应力数值模拟,同时考虑相变潜热及相变塑性的影响,用算例验证了模型的正确性,给出了不同时刻温度场分布及残余应力分布。

Numerical Simulation of Transient Thermal Features in the Remelting Processing of Stainless Steel

应用有限元方法对层流等离子体射流不锈钢表面重熔工艺中的瞬态热物理现象进行了数值模拟研究.针对不同加热距离,确定了材料熔化和凝固过程中的瞬态温度场、温度梯度和凝固率的时间和空间分布特征.通过引入等效温度面积密度概念,研究了不锈钢重熔热处理的适合条件.结果表明,9～13mm的范围是较为适宜的加热距离,该结果与试验观察基本符合.

Theory and Application of the Transient Injection Well Test

Based on the theory of the pumping well test, the transient injection well test was suggested in this paper. The design method and the scope of application are discussed in detail. The mathematical models are developed for the short-time and long-time transient injection test respectively. A double logarithm type curve matching method was introduced for analyzing the field transient injection test data. A set of methods for the transient injection test design, experiment performance and data analysis were established. Some field tests were analyzed, and the results show that the test model and method are suitable for the transient injection test and can be used to deal with the real engineering problems.

Non-Linear Wave-Induced Transient Response of Soil Around a Trenched Pipeline

Submarine pipelines are always trenched within a seabed for reducing wave loads and thereby enhancing their stability. Based on Biot’s poroelastic theory, a two-dimensional finite element model is developed to investigate non-linear wave-induced responses of soil around a trenched pipeline, which is verified with the flume test results by Sudhan et al. [Sudhan, C.M., Sundar, V., Rao, S.N., 2002. Wave induced forces around buried pipeline. Ocean Engineering, 29, 533–544] and Turcotte et al. [Turcotte, B.R., Liu, P.L.F., Kulhawy, F.H., 1984. Laboratory evaluation of wave tank parameters for wave-sediment interaction. Joseph H. Defree Hydraulic Laboratory Report 84-1, School of Civil and Environmental Engineering, Cornell University]. Non-linear wave-induced transient pore pressure around pipeline at various phases of wave loading is examined firstly. Unlike most previous investigations, in which only a single sediment layer and linear wave loading were concerned, in this study, the influences of the non-linearity of wave loading, the physical properties of backfill materials and the geometry profile of trenches on the excess pore pressures within the soil around pipeline, respectively, were explored, taking into account the in situ conditions of buried pipeline in the shallow ocean zones. Based on the parametric study, it is concluded that the shear modulus and permeability of backfill soils significantly affect the wave-induced excess pore pressures around trenched pipeline, and that the effect of wave non-linearity becomes more pronounced and comparable with that of trench depth, especially at high wave steepness in shallow water.

Numerical Solutions for the Transient Flow in the Homogenous Closed Circle Reservoirs

There are many fault block fields in China. A fault block field consists of fault pools. The small fault pools can be viewed as the closed circle reservoirs in some case. In order to know the pressure change of the developed formation and provide the formation data for developing the fault block fields reasonably, the transient flow should be researched. In this paper, we use the automatic mesh generation technology and the finite element method to solve the transient flow problem for the well located in the closed circle reservoir, especially for the well located in an arbitrary position in the closed circle reservoir. The pressure diffusion process is visualized and the well-location factor concept is first proposed in this paper. The typical curves of pressure vs time for the well with different well-location factors are presented. By comparing numerical results with the analytical solutions of the well located in the center of the closed circle reservoir, the numerical method is verified.

Transient natural ventilation of a space with localised heating

The natural ventilation of a well-mixed, pre-heated room with a point source of heating, and openings at the base and roof is investigated. The transient draining associated with the room being warmer than the exterior combined with the convective ow produced by the point source of heat leads to a fascinating series of transient ow regimes as the system evolves to the two-layer steady-state regime described by Linden, Lane-Ser_ and Smeed [1]. As the room begins to ventilate, a turbulent plume rises from the point source of heat to the ceiling, and typically forms a deepening layer of hot air. However, with a weak heat source, then at some point the ascending plume will intrude beneath the layer of original uid. Otherwise, the ascending plume always reaches the top of the room as the system evolves to a steady state. We develop a simpli_ed model of the transient evolution and test this with some new laboratory experiments. We conclude with a discussion of the implications of our results for real buildings.

Transient Ventilation Dynamics Following a Change in Strength of a Point Source of Heat

We investigate the transient ventilation flow within a confined ventilated space, with high- and low-level openings, when the strength of a low-level point source of heat is changed instantaneously. The steady-flow regime in the space involves a turbulent buoyant plume, which rises from the point source to a well-mixed warm upper layer. The steady-state height of the interface between this layer and the lower layer of exterior fluid is independent of the heat flux, but the upper layer becomes progressively warmer with heat flux. New analogue laboratory experiments of the transient adjustment between steady states identify that if the heat flux is increased, the continuing plume propagates to the top of the room forming a new, warmer layer. This layer gradually deepens, and as the turbulent plume entrains fluid from the original warm layer, the original layer is gradually depleted and disappears, and a new steady state is established. In contrast, if the source buoyancy flux is decreased, the continuing plume is cooler than the original plume, so that on reaching the interface it is of intermediate density between the original warm layer and the external fluid. The plume supplies a new intermediate layer, which gradually deepens with the continuing flow. In turn, the original upper layer becomes depleted, both as a result of being vented through the upper opening of the space, but also due to some penetrative entrainment of this layer by the plume, as the plume overshoots the interface before falling back to supply the new intermediate layer. We develop quantitative models which are in good accord with our experimental data, by combining classical plume theory with models of the penetrative entrainment for the case of a decrease in heating. Typically, we find that the effect of penetrative entrainment on the density of the intruding layer is relatively weak, provided the change in source strength is sufficiently large. However, penetrative entrainment measurably increases the rate at which the depth of the draining layer decreases. We conclude with a discussion of the importance of these results for the control of naturally ventilated spaces.

Numerical Simulation of Transient Thermal Field in Laser Melting Process

Numerical simulation of thermal field was studied in laser processing. The 3-D finite element model of transient thermal calculation is given by thermal conductive equation. The effects of phase transformation latent are considered. Numerical example is given to verify the model. Finally the real example of transient thermal field is given.

Transient Natural Ventilation of a Room with a Distributed Heat Source

We report on an experimental and theoretical study of the transient flows which develop as a naturally ventilated room adjusts from one temperature to another. We focus on a room heated from below by a uniform heat source, with both high- and low-level ventilation openings. Depending on the initial temperature of the room relative to (i) the final equilibrium temperature and (ii) the exterior temperature, three different modes of ventilation may develop. First, if the room temperature lies between the exterior and the equilibrium temperature, the interior remains well-mixed and gradually heats up to the equilibrium temperature. Secondly, if the room is initially warmer than the equilibrium temperature, then a thermal stratification develops in which the upper layer of originally hot air is displaced upwards by a lower layer of relatively cool inflowing air. At the interface, some mixing occurs owing to the effects of penetrative convection. Thirdly, if the room is initially cooler than the exterior, then on opening the vents, the original air is displaced downwards and a layer of ambient air deepens from above. As this lower layer drains, it is eventually heated to the ambient temperature, and is then able to mix into the overlying layer of external air, and the room becomes well-mixed. For each case, we present new laboratory experiments and compare these with some new quantitative models of the transient flows. We conclude by considering the implications of our work for natural ventilation of large auditoria.