Conceptual modelling and the project process in real simulation projects: a survey of simulation modellers

A survey was used to obtain information on the processes and methods used by simulation experts in real projects. The 102 survey respondents answered questions about their most recent simulation project. This paper presents some of the survey results, focussing mainly on conceptual modelling and the pattern of time allocation to different topics. There are a wide range of findings that include the modellers making changes to the initial conceptual model during subsequent tasks in most of the projects usually by adding complexity, model coding taking on average about twice the time of other topics, and the topics generally occurring in single blocks of time (at the resolution of the survey data collection) but with considerable overlaps. The results give an insight into the way experts approach simulation projects and their problem solving strategies. A potential application is in training novice modellers, particularly in developing ‘craft skills’. The results also provide an empirical basis for further research, especially in conceptual modelling.     

Probing the CH⋅⋅⋅π Weak Hydrogen Bond in Anesthetic Binding: The Sevoflurane–Benzene Cluster

Cooperativity between weak hydrogen bonds can be revealed in molecular clusters isolated in the gas phase. Here we examine the structure, internal dynamics, and origin of the weak intermolecular forces between sevoflurane and a benzene molecule, using multi‐isotopic broadband rotational spectra. This heterodimer is held together by a primary C? H???π hydrogen bond, assisted by multiple weak C? H???F interactions. The multiple nonbonding forces hinder the internal rotation of benzene around the isopropyl C? H bond in sevoflurane, producing detectable quantum tunneling effects in the rotational spectrum.     

Detoxifying CO2 Capture Reclaimer Waste by Anaerobic Digestion

The decrease in toxicity of carbon capture reclaimer monoethanolamine (MEA) waste (MEAw) during anaerobic degradation of such waste together with easily degradable organics was investigated. Samples were collected from a bioreactor at steady state with 86 % organic chemical oxygen demand removal at room temperature, which had been running on MEAw for 2 years. The toxicity of the digester effluents were 126, 42 and 10 times lower than that of the MEAw to the tested freshwater trophic groups of Pseudokirchneriella subcapitata, Daphnia magna and embryos of Danio rerio, respectively. The toxicity of the tested taxonomic groups after anaerobic digestion was mainly attributed to the ammonia generated by the degradation of MEAw.     

Analysis of the consistency of a mixed integer programming-based multi-category constrained discriminant model

Classification is concerned with the development of rules for the allocation of observations to groups, and is a fundamental problem in machine learning. Much of previous work on classification models investigates two-group discrimination. Multi-category classification is less-often considered due to the tendency of generalizations of two-group models to produce misclassification rates that are higher than desirable. Indeed, producing “good” two-group classification rules is a challenging task for some applications, and producing good multi-category rules is generally more difficult. Additionally, even when the “optimal” classification rule is known, inter-group misclassification rates may be higher than tolerable for a given classification model. We investigate properties of a mixed-integer programming based multi-category classification model that allows for the pre-specification of limits on inter-group misclassification rates. The mechanism by which the limits are satisfied is the use of a reserved judgment region, an artificial category into which observations are placed whose attributes do not sufficiently indicate membership to any particular group. The method is shown to be a consistent estimator of a classification rule with misclassification limits, and performance on simulated and real-world data is demonstrated.     

The characterization of the iron content of industrially cast aluminium

Pure intermetallic phases Al₁₃Fe₄, Al₆Fe, Al_mFe and Al_xFe have been extracted from Bridgman grown model aluminium–iron binary alloys by dissolving the aluminium matrix in butanol. Each phase has a distinct Mössbauer spectrum and variable temperature ⁵⁷Fe Mössbauer studies have enabled the Debye temperature of each phase to be determined. Hence, the variation of the recoilfree fraction f with temperature is determined for each phase. From this information it is possible to measure the proportion of each phase, either when the phases are extracted or in situ in aluminium. The results obtained can be used in the characterisation of industrially cast aluminium.     

"引力"七问

1 引力是什么 牛顿在17世纪就认识到宇宙中任何地方的一切物体的引力作用方式是相同的,且两物体间的吸引力与它们的质量的乘积成比例,与它们距离的平方成反比,即著名的"引力的平方反比律."爱因斯坦在20世纪初发表的广义相对论是研究物质在空间和时间中如何进行引力相互作用的理论,它将平方反比律解释成时空因物质和能量的存在而发生畸变的结果,并把牛顿理论包含在内.     

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.