Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence.     

Increased Rigidity in Complexes Formed from Negatively Charged Lariat Ethers and Alkali Metal Cations

Abstract

C-13 NMR longitudinal relaxation times have been measured for lariat ether complexes in which a negative charge is present in the ligand but the system is diamagnetic. A -CH₂COO^? group connected to the nitrogen of aza-15-crown-5 results in drastically increased T₁'s in the presence of Li⁺ compared to the values for the free carboxylic acid and for the acid in the presence of LiClO₄. Longer relaxation times upon complexation show the ‘cryptand-like’ behavior of the complexes, resulting from overall molecular reorientation rates due to compression. These conclusions are supported by molecular mechanics calculations described herein.     

Elastic Organic Crystals Based on Barbituric Derivative: Multi-faceted Bending and Flexible Optical Waveguide

Elastic organic single crystals with light-emitting and multi-faceted bending properties are extremely rare. They have potential application in optical materials and have attracted the extensive attention of researchers. In this paper, we reported a structurally simple barbituric derivative DBDT , which was easily crystallized and gained long needle-like crystals (centimeter-scale) in DCM/CH₃OH (v/v=2/8). Upon applying or removing the mechanical force, both the (100) and (040) faces of the needle-like crystal showed reversible bending behaviour, showing the nature of multi-faceted bending. The average hardness (H) and elastic modulus (E) were 0.28±0.01 GPa and 4.56±0.03 GPa for the (040) plane, respectively. Through the analysis of the single crystal data, it could be seen that the van der waals (C−H⋅⋅⋅π and C−H⋅⋅⋅C), H-bond (C−H⋅⋅⋅O) and π⋅⋅⋅π interactions between molecules were responsible for the generation of the crystal elasticity. Interestingly, elastic crystals exhibited optical waveguide characteristics in straight or bent state. The optical loss coefficients measured at 627 nm were 0.7 dBmm⁻¹ (straight state) and 0.9 dBmm⁻¹ (bent state), while the optical loss coefficient (α) were 1.5 dBmm⁻¹ (straight state) and 1.8 dBmm⁻¹ (bent state) at 567 nm. Notably, the elastic organic molecular crystal based on barbituric derivative could be used as the candidate for flexible optical devices.     

带凹性生产成本运输问题的新随机规划模型及其求解

提出了一种新的能反映决策者满意度的随机变量序关系,并据此研究了随机不等式的确定性等价类,方法被称为满意度方法.最后将其应用于带凹性生产成本运输问题的求解中,并将方法与常用的机会约束方法进行比较,说明满意度法不仅合理可行,而且当决策者对约束条件的要求越高时,它所得最优值越优于机会约束法所得最优值.     

Study of Polymer-Cement Composite Containing Portland Cement and Aqueous Poly (methyl methacrylate) Latex Polymer by Fourier-Transform Infrared (FT-IR) Spectroscopy

The polymer-cement composite is an immiscible band having modified morphology. Polymer phase improves the toughness of brittle cement and has a reinforcing effect, and interactions between cement components and polymers provide stability. In this study, polymer latex [poly(methyl methacrylate), PMMA] – cement paste was prepared with different weight proportions of polymer content. The main scientific objective of this report has been the analysis and the prediction of high strength with the aim of understanding the interactions of PMMA polymer with Portland cement after hydration reaction of cement pastes and curing the specimens for 28 days. The samples were studied by Fourier transform infrared (FT-IR) spectroscopy. The results are critically examined. It is shown that bands support the interaction of PMMA with cement in the composite.     

Ozone‐Induced Band Bending on Metal‐Oxide Surfaces Studied under Environmental Conditions

Ozone adsorption and decomposition on metal oxides is of wide interest in technology and in atmospheric chemistry. Here, ozone‐adsorption‐induced band bending is observed on Ti‐ and Fe‐oxide model surfaces under dry and humid conditions. Photoelectron spectroscopic studies indicate the effect of charge transfer to O₃, which limits the surface coverage of the precursor to decomposition reactions. This is also consistent with the negative pressure dependence observed in previous studies. These results contribute to our fundamental understanding of ozone adsorption and decomposition mechanisms on metal oxides of environmental and technological relevance.     

An Efficient One-Pot Synthesis of Nitriles from Carboxylic Acids Without Solvent Under Microwave Irradiation

Nitriles were prepared from alkyl and aryl carboxylic acids in dry media conditions, under microwave irradiation. Heating of the carboxylic acid, urea and amidosulfonic acid adsorbed on alumina support in a microwave oven affords nitriles in 20–93% yields.     

Resonant equations with the Neumann p-Laplacian plus an indefinite potential

We consider a nonlinear Neumann problem driven by the p  -Laplacian plus an indefinite potential and a Carathéodory reaction which at ±∞ is resonant with respect to any nonprincipal variational eigenvalue of the differential operator. Using critical point theory and Morse theory (critical groups), we show that the problem has at least three nontrivial smooth solutions, two of which have constant sign. In the process we prove some results of independent interest concerning the unique continuation property of eigenfunctions and the critical groups at infinity of a C¹$C^1$-functionals.     

循环流化床富氧气化实验研究

在循环流化床富氧气化实验台上,通过调节水蒸气流量使气化温度基本稳定在910℃,研究了不同氧气浓度及气化当量比对煤气组分、产气率、冷煤气效率及碳转化率的影响。结果表明,氧气浓度从25%增加至40%时,N2体积分数从48.82%降低至33.83%,H2从21.47%不断增加至27.59%,CH4基本不变;受水蒸气流量影响,氧气浓度高于35%时,CO体积分数降低,CO2体积分数增加;氧气浓度40%时的煤气热值为空气气化煤气热值的1.84倍,产气率随氧气浓度增加从2.35 m3/kg降至2.13 m3/kg,冷煤气效率和碳转化率不断增大;当气化当量比从0.20增加至0.29时,N2体积分数先降低后升高,H2体积分数从24.01%增加到25.46%后基本保持不变,CO和CH4持续减小,CO2不断增加,产气率由1.94 m3/kg升高到2.29 m3/kg;受水蒸气和气化当量比综合影响,冷煤气效率先增大后减小,碳转化率持续增加。     

Raman spectroscopy of CaM2+Ge2O6 (M2+ = Mg,Mn, Fe,Co, Ni,Zn) clinopyroxenes

The Raman spectra of Ge‐clinopyroxenes CaM²⁺Ge₂O₆ (M²⁺ = Mg, Mn, Fe, Co, Ni, Zn), general formula M2M1T₂O₆, are reported for the first time. Their spectral features are discussed in comparison with corresponding Si‐pyroxenes. The vibrational wavenumbers of germanates may be roughly obtained by a scale factor of about ~0.8 by those of the corresponding silicates, due to the Ge‐Si mass difference. The main peaks in the germanate Raman spectra at ~850 and ~540 cm⁻¹ may be related to Ge‐O tetrahedral stretching and chain bending, respectively; minor peaks between 200 and 400 cm⁻¹ are ascribed to bending and stretching of the non‐tetrahedral cations. Within Ge‐pyroxenes, possible correlations between crystallographic parameters and the vibrational wavenumbers are investigated. The main stretching mode at ~850 cm⁻¹ shows wavenumber changes with M²⁺ substitutions, but no simple correlation can be found with M²⁺ cation mass or size. On the other hand, the chain bending wavenumber linearly decreases with increasing ionic radius of the M²⁺ cation: the expansion of the M1 polyhedron reduces the chain kinking angle and the Ge‐Ge distances correspondingly increase. Copyright © 2015 John Wiley & Sons, Ltd.