cemff: A force field database for cementitious materials including validations, applications and opportunities
This paper reviews atomistic force field parameterizations for molecular simulations of cementitious minerals, such as tricalcium silicate (C3S), portlandite (CH), tobermorites (model C-S-H). Computational techniques applied to these materials include classical molecular simulations, density functional theory and energy minimization. Such simulations hold promise to capture the nanoscale mechanisms operating in cementitious materials and guide in performance optimization. Many force fields have been developed, such as Born–Mayer–Huggins, InterfaceFF (IFF), ClayFF, CSH-FF, CementFF, GULP, ReaxFF, and UFF. The benefits and limitations of these approaches are discussed and a database is introduced, accessible via a web-link (http://cemff.epfl.ch). The database provides information on the different force fields, energy expressions, and model validations using systematic comparisons of computed data with benchmarks from experiment and from ab-initio calculations. The cemff database aims at helping researchers to evaluate and choose suitable potentials for specific systems. New force fields can be added to the database.
To gain success in the evolutionary “arms race”, venomous animals such as scorpions produce diverse neurotoxins selected to hit targets in the nervous system of prey. Scorpion α-toxins affect insect and/or mammalian voltage-gated sodium channels (Nav’s) and thereby modify the excitability of muscle and nerve cells. Although more than a hundred α-toxins are known and a number of them have been studied into detail, the molecular mechanism of their interaction with Nav’s is still poorly understood. Here, we employ extensive molecular dynamics simulations and spatial mapping of hydrophobic/hydrophilic properties distributed over the molecular surface of α-toxins. It is revealed that in spite of the small size and relatively rigid structure, these toxins possess modular organization from structural, functional and evolutionary perspectives. The more conserved and rigid “core module” is supplemented with the “specificity module” (SM) that is comparatively flexible and variable, and determines the taxon (mammal vs. insect) specificity of α-toxin activity. We further show that SMs in mammal toxins are more flexible and hydrophilic than in insect toxins. Concomitant sequence-based analysis of Nav’s extracellular loops suggests that α-toxins recognize the channels using both modules. We propose that the core module binds to the voltage-sensing domain of repeat IV, whereas the more versatile SM interacts with the pore domain in repeat I of Nav’s. These findings corroborate and expand the hypothesis on different functional epitopes of toxins that has been reported previously. In effect, we propose that the modular structure in toxins evolved to match the domain architecture of Nav’s.
Molecular-level knowledge of the thermodynamic, structural, and transport properties of water confined by interfaces and nanopores of various materials is crucial for quantitative understanding and prediction of many natural and technological processes, including carbon sequestration, water desalination, nuclear waste storage, cement chemistry, fuel cell technology, etc. Computational molecular modeling is capable to significantly complement the experimental investigations of such systems by providing invaluable atomic-scale information leading to improved understanding of the specific effects of the substrate structure and composition on the structure, dynamics and reactivity of interfacial and nano-confined aqueous solutions. This paper offers a brief overview of recent efforts to quantify some of these effects for individual H2O molecules and hydrated ions confined at the interfaces and in nanopores of several typical hydrophilic and hydrophobic materials. The first molecular layer of aqueous solution at all substrates is often highly ordered, indicating reduced translational and orientational mobility of the H2O molecules. This ordering cannot be simply described as “ice-like”, but rather resembles the behavior of supercooled water or amorphous ice, although with very significant substrate-specific variations.
Mutations in transmembrane (TM) domains of receptor tyrosine kinases are shown to cause a number of inherited diseases and cancer development. Here, we use a combined molecular modeling approach to understand molecular mechanism of effect of G370R and A391E mutations on dimerization of TM domains of human fibroblast growth factor receptor 3 (FGFR3). According to results of Monte-Carlo conformational search in the implicit membrane and further molecular dynamics simulations, TM dimer of this receptor is able to form a number of various conformations, which differ significantly by the free energy of association in a full-atom model bilayer. The aforementioned mutations affect dimerization efficiency of TM segments and lead to repopulation of conformational ensemble for the dimer. Particularly, both mutations do not change the dimerization free energy of the predominant (putative “non-active”) symmetric conformation of TM dimer, while affect dimerization efficiency of its asymmetric (“intermediate”) and alternative symmetric (putative “active”) models. Results of our simulations provide novel atomistic prospective of the role of G370 and A391E mutations in dimerization of TM domains of FGFR3 and their consecutive contributions to the activation pathway of the receptor.
Ribosomal protein S2 is an essential component of translation machinery, and its viable mutated variants conferring distinct phenotypes serve as a valuable tool in studying the role of S2 in translation regulation. One of a few available rpsB mutants, rpsB1, shows thermosensitivity and ensures enhanced expression of leaderless mRNAs. In this study, we identified the nature of the rpsB1 mutation. Sequencing of the rpsB1 allele revealed a G-to-A transition in the part of the rpsB gene which encodes a coiled-coil domain of S2. The resulting E132K substitution resides in a highly conserved site, TKKE, a so-called N-terminal capping box, at the beginning of the second alpha helix. The protruding coiled-coil domain of S2 is known to provide binding with 16S rRNA in the head of the 30S subunit and, in addition, to interact with a key mRNA binding protein, S1. Molecular dynamics simulations revealed a detrimental impact of the E132K mutation on the coiled-coil structure and thereby on the interactions between S2 and 16S rRNA, providing a clue for the thermosensitivity of the rpsB1 mutant. Using a strain producing a leaderless lacZ transcript from the chromosomal lac promoter, we demonstrated that not only the rpsB1 mutation generating S2/S1-deficient ribosomes but also the rpsA::IS10 mutation leading to partial deficiency in S1 alone increased translation efficiency of the leaderless mRNA by about 10-fold. Moderate overexpression of S1 relieved all these effects and, moreover, suppressed the thermosensitive phenotype of rpsB1, indicating the role of S1 as an extragenic suppressor of the E132K mutation.
This edition presents abstracts of the reports of the participants of the VI International conference "Advanced materials and technologies - 2014"
A method based on the spectral analysis of thermowave oscillations formed under the effect of radiation of lasers operated in a periodic pulsed mode is developed for investigating the state of the interface of multilayered systems. The method is based on high sensitivity of the shape of the oscillating component of the pyrometric signal to adhesion characteristics of the phase interface. The shape of the signal is quantitatively estimated using the correlation coefficient (for a film–interface system) and the transfer function (for multilayered specimens).
Let G be a semisimple algebraic group whose decomposition into the product of simple components does not contain simple groups of type A, and P⊆G be a parabolic subgroup. Extending the results of Popov , we enumerate all triples (G, P, n) such that (a) there exists an open G-orbit on the multiple flag variety G/P × G/P × . . . × G/P (n factors), (b) the number of G-orbits on the multiple flag variety is finite.
I give the explicit formula for the (set-theoretical) system of Resultants of m+1 homogeneous polynomials in n+1 variables