关键词： Ordinary differential equations   Numerical integration   Energy-preserving methods   MB4 method   Nonlinear Schrodinger equation   Parallel computing  

摘要： In simulating physical systems, conservation of the total energy is often essential, especially when energy conversion between different forms of energy occurs frequently. Recently, a new fourth order energy-preserving integrator named MB4 was proposed based on the so-called continuous stage Runge-Kutta methods (Miyatake and Butcher in SIAM J Numer Anal 54(3):1993-2013, 2016). A salient feature of this method is that it is parallelizable, which makes its computational time for one time step comparable to that of second order methods. In this paper, we illustrate how to apply the MB4 method to a concrete ordinary differential equation using the nonlinear Schrodinger-type equation on a two-dimensional grid as an example. This system is a prototypical model of two-dimensional disordered organic material and is difficult to solve with standard methods like the classical Runge-Kutta methods due to the nonlinearity and the delta-function like potential coming from defects. Numerical tests show that the method can solve the equation stably and preserves the total energy to 16-digit accuracy throughout the simulation. It is also shown that parallelization of the method yields up to 2.8 times speedup using 3 computational nodes.

关键词： Aluminum alloys   Precipitation kinetics   Atom-probe tomography   Elevated-temperature  

摘要： A micro-addition (0.025 at.%) of slow-diffusing W to an Al-0.26Mn-0.11Mo-0.11Si-0.08Zr-0.02Sc-0.01Er (at.%) alloy accelerates L1(2)-Al-3(Zr,Sc) precipitation but retards alpha-Al(Mn,Mo)Si precipitation. The W micro-addition increases the peak-microhardness of the alloy during isothermal aging but does not improve the coarsening resistance and creep resistance.

关键词： Hydrogenated defective graphene   Exothermic H-2 desorption   Density functional theory   Molecular dynamics simulations   Activation barrier   Tensile strength  

摘要： A combined density functional theory and molecular dynamics approach is employed to study modifications of graphene at atomistic level for better H-2 storage. The study reveals H-2 desorption from hydrogenated defective graphene structure, V-222, to be exothermic. H-2 adsorption and desorption processes are found to be more reversible for V-222 as compared to pristine graphene. Our study shows that V-222 undergoes brittle fracture under tensile loading similar to the case of pristine graphene. The tensile strength of V-222 shows slight reduction with respect to their pristine counterpart, which is attributed to the transition of sp(2) to sp(3)-like hybridization. The study also shows that the V-222 structure is mechanically more stable than the defective graphene structure without chemically adsorbed hydrogen atoms. The current fundamental study, thus, reveals the efficient recovery mechanism of adsorbed hydrogen from V-222 and paves the way for the engineering of structural defects in graphene for H-2 storage. (C) 2020 The Author(s). Published by Elsevier Ltd on behalf of Hydrogen Energy Publications LLC.

关键词： Transition states   Chemical reactions   Solvents   Ab initio molecular dynamics   Post-translational modification  

摘要： We report a computational approach to evaluate the reaction mechanisms of glycosylation using ab initio molecular dynamics (AIMD) simulations in explicit solvent. The reaction pathways are simulated via free energy calculations based on metadynamics and trajectory simulations using Born-Oppenheimer molecular dynamics. We applied this approach to investigate the mechanisms of the glycosylation of glucosyl alpha-trichloroacetimidate with three acceptors (EtOH, i-PrOH, and t-BuOH) in three solvents (ACN, DCM, and MTBE). The reactants and the solvents are treated explicitly using density functional theory. We show that the profile of the free energy surface, the synchronicity of the transition state structure, and the time gap between leaving group dissociation and nucleophile association can be used as three complementary indicators to describe the glycosylation mechanism within the S(N)1/S(N)2 continuum for a given reaction. This approach provides a reliable means to rationalize and predict reaction mechanisms and to estimate lifetimes of oxocarbenium intermediates and their dependence on the glycosyl donor, acceptor, and solvent environment.

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.