Multiresolution molecular mechanics: A unified and consistent framework for general finite element shape functions

We present a general mathmatical framework for the newly proposed energy-based concurrent atomistic/continuum method Multiresolution Molecular Mechanics (MMM) The main features of the generalized framework are: (i) Consistency with the atomistic framework by directly employing the interatomic potential to calculate force and energy; (ii) Simple procedure for analytically deriving the optimal summation rule for any given finite element shape function employed in the coarse-grained region. The procedure for obtaining the optimal summation rule is developed based on deriving and then fitting the atomic energy distribution within an element under the constraint of a given shape function. To validate the generalized framework, test problems including nonlocal harmonic and anharmonic models undergoing tensile, shear and bending deformations will be solved using linear, bilinear and quadratic elements, respectively. Results obtained using the proposed optimal summation rules for the different element types will be compared with Gauss quadrature for accuracy. Through error structure analyses, it is found that the proposed summation rule always outperforms Gauss quadrature, even when the later employs more quadrature points than the former. It is argued that widely-used numerical quadrature techniques such as Gauss quadrature are not optimal for coarse-grained atomic energy approximation because they do not account for the discrete nature of the atoms. In contrast, the present summation rule is derived consistently from the underlying atomic energy distribution, and thus has better accuracy and smaller computational cost. REFERENCE [1] Yang, Q., Biyikli, E., To, A.C. Comput. Methods Appl. Mech. Eng. 2013, 258, 26‑38

Multiresolution molecular mechanics: surface effects and iso-parametric analysis

Within the generalized framework of the newly presented energy-based concurrent atomistic/continuum method Multiresolution Molecular Mechanics (MMM) [1], two proposed summation rules, the bulk summation and the edge summation rule to efficiently determine the bulk and surface energy distribution respectively, consists the optimal MMM summation rule. In Ref. [1], the bulk summation rule has been verified and proved to outperform the widely used Gauss quadrature. In this study, the edge summation rule will be employed to specifically capture surface effects. This is achieved in three steps: (i) use the edge summation rule to determine the surface energy distribution for any given finite element method (FEM) shape function analytically; (ii) select the optimal number of surface primary sampling atoms on the surfaces, and (iii) determine the weight for each surface primary sampling atoms using the edge summation rule and then use their energies to sampling the surface energy. In particular, the effect of the selection of surface primary sampling atoms on the accuracy of capturing surface effect will be studied. In addition, the sampling errors introduced by employing the edge summation rule will be determined through error structure analysis. Then iso-parametric analysis within the generalized framework of MMM will be performed to standardize the implementation procedure of MMM, as is widely employed in conventional FEM. The iso-parametric analysis is achieved by performing the surface summation rule and the bulk summation rule within some specifically designed surface parent elements and bulk parent elements. In particular, the iso-parametric analysis will be performed with respect to linear, bilinear, and quadratic elements undergoing tensile, shear, and bending deformations and will be compared against full atomistic to show the effectiveness of MMM. REFERENCES [1] Yang, Q., To, A.C. Multiresolution molecular mechanics: a unified and consistent framework for general finite element shape functions. Comp. Meth. Appl. Mech. Eng. (under review). [2] Yang, Q., Biyikli, E., To, A.C. Multiresolution molecular mechanics: statics. Comp. Meth. Appl. Mechanics Eng. 2013, 258, 26‑38. [3] Yang, Q., Biyikli, E., To, A.C. Multiresolution molecular mechanics: convergence and error structure analysis. Comp. Meth. Appl. Mech. Eng. 2014, 269, 20‑45 . [4] Biyikli, E., Yang, Q., To, A.C. Multiresolution molecular mechanics: dynamics. Comp. Meth. Appl. Mech. Eng. 2014, 274, 42‑55

MULTIRESOLUTION MOLECULAR MECHANICS: THEORY AND APPLICATIONS

A general mathematical framework, Multiresolution Molecular Mechanics (MMM), is proposed to consistently coarse-grain molecular mechanics at different resolutions in order to extend the length scale of nanoscale modeling of crystalline materials. MMM is consistent with molecular mechanics in the sense that the constitutive description such as energy and force calculations is exactly the same as molecular mechanics and no empirical and phenomenological constitutive relationships in continuum mechanics are employed. As such, MMM can converge to full molecular mechanics naturally. As many coarse-graining approaches, MMM is based on approximating the total potential energy of a full atomistic model. Analogous to quadrature rules employed to evaluate energy integrals in finite element method (FEM), a summation rule is required to evaluate finite energy summations. Most existing summation rules are specifically designed for the linear interpolation shape function and their extensions to high order shape functions are currently not clear. What distinguishes MMM from existing works is that MMM proposes a novel summation rule framework SRMMM that is valid and consistent for general shape functions. The key idea is to analytically derive the energy distribution of the coarse-grained atomistic model and then choose some quadrature-type (sampling) atoms to accurately represent the derived energy distribution for a given shape function. The optimal number, weight and position of sampling atoms are also determined accordingly, similar to the Gauss quadrature in FEM. The governing equations are then derived following the variational principle. The proposed SRMMM is verified and validated numerically and compared against many other summation rules such as Gauss-quadrature-like rule. And SRMMM demonstrates better performance in terms of accuracy and computational cost. The convergence property of MMM is also studied numerically and MMM shows FEM-like behavior under certain circumstance. In addition, MMM has been applied to solve problems such as crack propagation, atomic sheet shear, beam bending and surface relaxations by employing high order interpolation shape functions in one (1D), two (2D) and three dimensions (3D)

A method integrating simulation and reinforcement learning for operation scheduling in container terminals

The objective of operation scheduling in container terminals is to determine a schedule that minimizes time for loading or unloading a given set of containers. This paper presents a method integrating reinforcement learning and simulation to optimize operation scheduling in container terminals. The introduced method uses a simulation model to construct the system environment while the Q-learning algorithm (reinforcement learning algorithm) is applied to learn optimal dispatching rules for different equipment (e.g. yard cranes, yard trailers). The optimal scheduling scheme is obtained by the interaction of the Q-learning algorithm and simulation environment. To evaluate the effectiveness of the proposed method, a lower bound is calculated considering the characteristics of the scheduling problem in container terminals. Finally, numerical experiments are provided to illustrate the validity of the proposed method

A lexicographic optimization approach for berth schedule recovery problem in container terminals

In container terminals, the planned berth schedules often have to be revised because of disruptions caused by severe weather, equipment failures, technical problems and other unforeseen events. In this paper, the problem of berth schedule recovery is addressed to reduce the influences caused by disruptions. A multi-objective, multi-stage model is developed considering the characteristics of different customers and the trade-off of all parties involved. An approach based on the lexicographic optimization is designed to solve the model. Numerical experiments are provided to illustrate the validity of the proposed Model A and algorithms. Results indicate that the designed Model A and algorithm can tackle the berth plan recovery problem efficiently because the beneficial trade-off among all parties involved are considered. In addition, it is more flexible and feasible with the aspect of practical applications considering that the objective order can be adjusted by decision makers

Modeling the sailing risk of RoPax ships with Bayesian Network

In this paper, a methodology based on Bayesian Network (BN) was proposed to deal with the difficulty of risk analysis in RoPax transport. Based on data collection and expert survey, BN model for RoPax sailing risk analysis was constructed first. Then the Expectation Maximization (EM) algorithm for parameter learning and Evidence Prepropagation Importance Sampling (EPIS) algorithm for reasoning were designed. Finally, a sensitivity analysis was conducted. To validate the model algorithms, a case study on the RoPax system of Bohai gulf in China was provided. Results indicate that the BN model can effectively address the problem of data deficiency and mutual dependency of incidents in risk analysis. It can also model the development process of unexpected hazards and provide decision support for risk mitigation. First published online: 10 Sep 201

Trichostatin A destabilizes HIF-2α through a VHL-independent but proteasome-dependent pathway in cancer cell lines and tumor xenografts

Histone deacetylase (HDACs) inhibitors are a new generation of anti-cancer agents. Little is known regarding the effect of HDAC inhibitors on HIF-2α. The effect of trichostatin A (TSA), a class I/II HDAC inhibitor, on HIF-2α protein expression was investiagted in cancer cell lines and tumor xenografts. Results showed TSA inhibited the HIF-2α protein expression in a dose-dependent manner, which was VHL-independent, but proteasome-dependent in cell lines. In tumor xenografts, TSA inhibited tumor growth and HIF-2α expression. Knocking down of HDAC6 by small RNA interfering decreased HIF-2α protein expression. HDAC6 physically interracted with HIF-2α, and HIF-2α was acetylated by TSA. TSA destabilizes HIF-2α in a proteasome dependent manner, which is unrelated to VHL, suggesting the anticancer effect of TSA is at least partially mediated by its inhibition of HIF-2α, which provides a new insight into the molecular mechanism underlying the anticancer effect of HDAC inhibitors

Numerical investigation of cycle performance in compressed air energy storage in aquifers

Compressed air energy storage (CAES) is one of the promising technologies to store the renewable energies such as surplus solar and wind energy in a grid scale. Due to the widespread of aquifers in the world, the compressed air energy storage in aquifers (CAESA) has advantages compared with the compressed air energy storage in caverns and air tanks. The feasibility of aquifers as storage media in CAES system has been demonstrated by numerical models and field tests. This study proposes a numerical model by Transport of Unsaturated Groundwater and Heat Version 3.0/Equation-of-State 3 (TOUGH3/EOS3) to simulate a field-scale study of a novel CAES by storing the compressed air in aquifers. The feasibility of the model has been demonstrated by comparison of simulation results and monitoring data. After that, three types of cycles, which are daily cycle, weekly cycle and monthly cycle, are designed to study their performance within a month working cycle. Their gas saturation show small differences after one month cycle. When the air with temperature of 50 °C injected into aquifers with temperature of 20 °C, after the cycle finished, the air temperature in aquifer of daily cycle are 5.4 °C higher than that of weekly cycle and 10.8 °C higher than that of monthly cycle. It is indicated that during the same cycle periods, the more cycle times, the higher air temperature in aquifers after the cycle. The energy recovery efficiencies for daily cycle, weekly cycle and monthly cycle are 96.96%, 96.27% and 93.15%, respectively. The slight increase of energy recovery efficiencies from daily cycle to monthly cycle indicate that with the same energy storage scales, the energy produced by daily cycle has slight competitiveness. The simulation results can provide references for engineering application in future

Effectiveness of intravenous r-tPA versus UK for acute ischaemic stroke: a nationwide prospective Chinese registry study

BACKGROUND Intravenous recombinant tissue plasminogen activator (r-tPA) and urokinase (UK) are both recommended for the treatment of acute ischaemic stroke (AIS) in China, but with few comparative outcome data being available. We aimed to compare the outcomes of these two thrombolytic agents for the treatment of patients within 4.5 hours of onset of AIS in routine clinical practice in China. METHODS A pre-planned, prospective, nationwide, multicentre, real-world registry of consecutive patients with AIS (age ≥18 years) who received r-tPA or UK within 4.5 hours of symptom onset according to local decision-making and guideline recommendations during 2017-2019. The primary effectiveness outcome was the proportion of patients with an excellent functional outcome (defined by modified Rankin scale scores 0 to 1) at 90 days. The key safety endpoint was symptomatic intracranial haemorrhage according to standard definitions. Multivariable logistic regression was used for comparative analysis, with adjustment according to propensity scores to ensure balance in baseline characteristics. RESULTS Overall, 4130 patients with AIS were registered but 320 had incomplete or missing data, leaving 3810 with available data for analysis of whom 2666 received r-tPA (median dose 0.88 (IQR 0.78-0.90) mg/kg) and 1144 received UK (1.71 (1.43-2.00)×10 international unit per kilogram). There were several significant intergroup differences in patient characteristics: r-tPA patients were more educated, had less history of stroke, lower systolic blood pressure, greater neurological impairment and shorter treatment times from symptom onset than UK patients. However, in adjusted analysis, the frequency of excellent outcome (OR 1.18, 95% CI 1.00 to 1.40, p=0.052) and symptomatic intracranial haemorrhage (OR 0.70, 95% CI 0.33 to 1.47, p=0.344) were similar between groups. CONCLUSIONS UK may be as effective and carry a similar safety profile as r-tPA in treating mild to moderate AIS within guidelines in China. REGISTRATION: http://www.clinicaltrials.gov. unique identifier: NCT02854592