关键词： Na+   H2O   Coal gangue-based geopolymer   Molecular structure   Mechanical properties   Molecular dynamics simulation  

摘要： The aim of this work is to study the impacts of Na+ and H2O on structural and mechanical properties of coal gangue-based geopolymer by experiment and molecular dynamics. Geopolymers were prepared by coal gangue and mixed solution of NaOH and water glass. Then X-ray fluorescence (XRF) and X-ray diffraction (XRD) were utilized to characterize the main chemical composition and crystalline phase of geopolymer after 28d curing. Moreover, Na2Si2O5 glass was firstly proposed to establish the molecular structure of geopolymers with different Na/Al and H2O/Al. Structural optimization and molecular dynamics simulation were implemented under the specific force field. Simulated XRD pattern, energy and temperature curves, radial distribution function (RDF), hydrogen bond, bond angle distribution, mean square displacement (MSD) and elastic modulus of geopolymer were calculated and analyzed. Results indicated that with the increase of Na+ and H2O content, structure of geopolymer became more stable and mechanical properties were improved significantly. (C) 2020 Elsevier Ltd. All rights reserved.

关键词： molecular chaperone   Cdc37   Cdk4   kinase maturation   molecular dynamics  

摘要： The Hsp90 chaperone system interacts with a wide spectrum of client proteins, forming variable and dynamic multiprotein complexes that involve the intervention of cochaperone partners. Recent results suggest that the role of Hsp90 complexes is to establish interactions that suppress unwanted client activities, allow clients to be protected from degradation and respond to biochemical signals. Cryo-electron microscopy (cryoEM) provided the first key molecular picture of Hsp90 in complex with a kinase, Cdk4, and a cochaperone, Cdc37. Here, we use a combination of molecular dynamics (MD) simulations and advanced comparative analysis methods to elucidate key aspects of the functional dynamics of the complex, with different nucleotides bound at the N-terminal Domain of Hsp90. The results reveal that nucleotide-dependent structural modulations reverberate in a striking asymmetry of the dynamics of Hsp90 and identify specific patterns of long-range coordination between the nucleotide binding site, the client binding pocket, the cochaperone and the client. Our model establishes a direct atomic-resolution cross-talk between the ATP-binding site, the client region that is to be remodeled and the surfaces of the Cdc37-cochaperone. (C) 2020 Elsevier Ltd. All rights reserved.

关键词： Neuronal network models   Antennal lobe dynamics   Computational neuroscience   Olfactory modeling  

摘要： Odors emanating from a biologically relevant source are rapidly embedded within a windy, turbuluent medium that folds and spins filaments into fragmented strands of varying sizes. Environmental odor plumes therefore exhibit complex spatiotemporal dynamics, and rarely yield an easily discernible concentration gradient marking an unambiguous trail to an odor source. Thus, sensory integration of chemical input, encoding odor identity or concentration, and mechanosensory input, encoding wind speed, is a critical task that animals face in resolving the complex dynamics of odor plumes and tracking an odor source. In insects, who employ olfactory navigation as their primary means of foraging for food and finding mates, the antennal lobe (AL) is the first brain structure that processes sensory odor information. Although the importance of chemosensory and mechanosensory integration is widely recognized, the AL itself has traditionally been viewed purely from the perspective of odor encoding, with little attention given to its role as a bimodal integrator. In this work, we seek to explore the AL as a model for studying sensory integration - it boasts well-understood architecture, well-studied olfactory responses, and easily measurable cells. Using a moth model, we present experimental data that clearly demonstrates that AL neurons respond, in dynamically distinct ways, to both chemosensory and mechanosensory input;mechanosensory responses are transient and temporally precise, while olfactory responses are long-lasting but lack temporal precision. We further develop a computational model of the AL, show that our model captures odor response dynamics reported in the literature, and examine the dynamics of our model with the inclusion of mechanosensory input;we then use our model to pinpoint dynamical mechanisms underlying the bimodal AL responses revealed in our experimental work. Finally, we propose a novel hypothesis about the role of mechanosensory input in sculpting AL dyna

关键词： Peptides and proteins   Genetics   Nanoparticles   Fuels   Computational chemistry  

摘要： Dynamic DNA walkers can move cargoes on a surface through various mechanisms including enzymatic reactions and strand displacement. While they have demonstrated high processivity and speed, their motion dynamics are not well understood. Here, we utilize an enzyme-powered DNA walker as a model system and adopt a random walk model to provide new insight into migration dynamics. Four distinct migration modes (ballistic, Levy, self-avoiding, and diffusive motions) are identified. Each mode shows unique step time and velocity distributions, which are related to mean-squared displacement (MSD) scaling. Experimental results are in excellent agreement with the theoretical predictions. With a better understanding of the dynamics, we performed a mechanistic study, elucidating the effects of cargo types and sizes, walker sequence designs, and environmental conditions. Finally, this study provides a set of design principles for tuning the behaviors of DNA walkers. The DNA walkers from this work could serve as a versatile platform for mathematical studies and open new opportunities for bioengineering.

关键词： Urea  

摘要： We herein report an ab initio molecular dynamics study on a natural DES composed of urea and betaine in a 3 : 2 ratio, as a test case for evaluating the water effect. The article deals with a theoretical study using both ab initio molecular dynamics and quantum chemistry computations in order to unravel the role of water in the nanostructure of a urea-betaine mixture. Preliminary molecular dynamics outcomes (both radial and spatial distribution functions) suggest that water promotes the association between urea and betaine by increasing the hydrogen bond network and precluding the aggregation of urea molecules. In other words, the presence of water allows a less restrictive hydrogen bond network, presenting a regimen where the strong hydrogen bond interactions are replaced by a wide variety of weaker hydrogen bond interactions. On the other hand, in a water free DES there is a regimen where strong urea-betaine interactions are dominant. It is shown that second order perturbation theory energy analysis provides cogent insights into charge spreading and hydrogen bond patterns. A vibrational analysis (both IR and power spectrum) over the ab initio molecular dynamics trajectories in the water free DES as well as in the urea-betaine-water systems reveals that our results are consistent with the second order perturbation theory analysis and with the hydrogen bond network pattern.

关键词： Redox reactions   Metals   Ligands   Catalysts   Quantum mechanics  

摘要： Both [Co-II(qpy)(H2O)(2)](2+) and [Fe-II(qpy)(H2O)(2)](2+) (with qpy = 2,2':6',2 '':6 '',2'''-quaterpyridine) are efficient homogeneous electrocatalysts and photoelectrocatalysts for the reduction of CO2 to CO. The Co catalyst is more efficient in the electrochemical reduction, while the Fe catalyst is an excellent photoelectrocatalyst ( ACS Catal. 2018, 8, 3411-3417). This work uses density functional theory to shed light on the contrasting catalytic pathways. While both catalysts experience primarily ligand-based reductions, the second reduction in the Co catalyst is delocalized onto the metal via a metal-ligand bonding interaction, causing a spin transition and a distorted ligand framework. This orbital interaction explains the experimentally observed mild reduction potential and slow kinetics of the second reduction. The decreased hardness and doubly occupied d(z2)-orbital facilitate a sigma-bond with the CO2-pi* in an eta(1)-kappa C binding mode. CO2 binding is only possible after two reductions resulting in an EEC mechanism (E = electron transfer, C = chemical reaction), and the second protonation is rate-limiting. In contrast, the Fe catalyst maintains a Lewis acidic metal center throughout the reduction process because the metal orbitals do not strongly mix with the qpy-pi* orbitals. This allows binding of the activated CO2 in an eta(2)-binding mode. This interaction stabilizes the activated CO2 via a pi-type interaction of a Fe-t(2g) orbital and the CO2-pi* and a dative bond of the oxygen lone pair. This facilitates CO2 binding to a singly reduced catalyst resulting in an ECE mechanism. The barrier for CO2 addition and the second protonation are higher than those for the Co catalyst and rate-limiting.

关键词： Shape-memory polyurethane   Semi-crystalline polymer   Polymer crystallization   Multiscale simulation   Coarse-grained molecular dynamics simulation   Melting temperature   Thermo-mechanical deformation  

摘要： Shape-memory polyurethanes (SMPUs) are smart semi-crystalline polymers with heat-induced shape memory. The segmented SMPU copolymer simulated in this study consisted of an isocyanate (hard segment) that acts as a netpoint to stabilize the network, and a polyol (soft segment) that, owing to polymer crystallization, acts as a molecular switch. The ratio of hard to soft segments is a determining factor in the thermo-mechanical behavior and shape-memory performance of SMPU copolymers. However, the limitations of the scale of the conventional all-atom molecular dynamics simulation makes it difficult to observe mesoscale phenomena such as the phase-segregated morphology and polymer crystallization. To address this problem, we have developed a coarse-grained (CG) molecular dynamics (MD) model with fewer degrees of freedom by treating multiple atoms as a single bead. We derived the CG intra- and inter-bead potentials of the CG MD model such that the structural and thermodynamic properties would be identical to those of the all-atom reference model. Consequently, polymer crystallization was verified to occur at room temperature with the developed CG potentials. We subsequently investigated the effects of hard-segment content (HSC) on the thermal transition at SMPU melting temperature. We also investigated the influence of HSC on the thermo-elastic behavior and shape-memory properties of SMPU copolymers by simulating a 4-step thermo-mechanical cycle. The results revealed that the microstructure significantly affects macroscopic shape-memory behavior. We expect that this study will be used to improve the prediction and design of the thermo-mechanical behavior of segmented polyurethane or other semi-crystalline polymers.

摘要： The high sensitivity and effective frequency discrimination of sound detection performed by the auditory system rely on the dynamics of a system of hair cells. In the inner ear, these acoustic receptors are primarily attached to an overlying structure that provides mechanical coupling between the hair bundles. Although the dynamics of individual hair bundles has been extensively investigated, the influence of mechanical coupling on the motility of the system of bundles remains underdetermined. We developed a technique of mechanically coupling two active hair bundles, enabling us to probe the dynamics of the coupled system experimentally. We demonstrated that the coupling could enhance the coherence of hair bundles' spontaneous oscillation, as well as their phase-locked response to sinusoidal stimuli, at the calcium concentration in the surrounding fluid near the physiological level. The empirical data were consistent with numerical results from a model of two coupled nonisochronous oscillators, each displaying a supercritical Hopf bifurcation. The model revealed that a weak coupling can poise the system of unstable oscillators closer to the bifurcation by a shift in the critical point. In addition, the dynamics of strongly coupled oscillators far from criticality suggested that individual hair bundles may be regarded as nonisochronous oscillators. An optimal degree of nonisochronicity was required for the observed tuning behavior in the coherence of autonomous motion of the coupled system.

关键词： Tungsten   Graphene   Helium   Diffusion   Point defects   First principles calculation  

摘要： In Tokamak device, helium atoms caused by the fusion reaction will generate helium bubbles and point defects after entering the first wall material composed of tungsten metal, which will seriously affect the stability of the first wall material. Therefore, we designed the tungsten/graphene/tungsten interface material as a new first wall material. It was found from first-principles calculations that the interface can trap helium atoms to reduce the diffusion of helium atoms from the interface to the tungsten phase again. The interface also traps vacancies and accelerates the recombination of vacancies and self-interstitial atoms. Using the quasi-harmonic Debye model, we found that the presence of the graphene layer can also improve the ductility, at a cost of reducing the mechanical modulus of the tungsten metal. (C) 2020 Elsevier B.V. All rights reserved.

关键词： C-S-Hs-PCE   Sodium sulfate   Hydration kinetics   Mechanical properties  

摘要： This study reports the effects of combined application of calcium silicate hydrate seed-Polycarboxylate (C-S-Hs-PCE) and sodium sulfate (SS) on the hydration kinetics and mechanical properties of cement paste. The setting time, compressive and flexural strengths, and chemical shrinkage were evaluated. The mechanism of synergistic utilization of C-S-Hs-PCE and SS was explored on basis of the hydration heat releases, pore structures and crystalline phases. The results show that the setting time is shortened and the strengths of cement pastes are improved dramatically with the addition of C-S-Hs-PCE and SS. The incorporation of C-S-Hs-PCE increases the chemical shrinkage, while the co-doped C-S-Hs-PCE and SS can mitigate it. Overall, it accelerates the hydration process especially at early age, the pore structures are refined and the volume of gel micro pores increases due to more formation of gel. In the hardened pastes, the content of calcium hydroxide (CH) increases with the C-S-Hs-PCE and SS dosages, attributed to the further hydration of dicalcium silicate (C2S) and tricalcium silicate (C3S). This study could be viewed as a reference for the application of C-S-Hs-PCE and SS in cement paste, which is of great significance for its enhancement of early strengths. (C) 2020 Elsevier Ltd. All rights reserved.