Improved sampling in Monte Carlo simulations of small clusters

In this thesis, improved sampling algorithms are applied to atomic and molecular clusters. The parallel-tempering Monte Carlo procedure is used to characterize the (CO2)n, n = 6, 8, 13, 19, and 38, clusters. The heat capacity curves of the n = 13 and 19 clusters are found to have pronounced peaks that can be associated with cluster melting. In addition, there is evidence of a low temperature "solid -> solid" transition in the case of (CO2)19. The low-energy minima and rearrangement pathways are determined and used to examine the complexity of the potential energy surfaces of the clusters. An algorithm combining the Tsallis generalized ensemble and the parallel tempering algorithm is introduced and applied to a 1D model potential and to Ar38. The convergence of parallel tempering Monte Carlo simulations of the 38-atom Lennard-Jones cluster starting from the Oh global minimum and from the C5v second lowest-energy minimum is also investigated. It is found that achieving convergence is appreciably more difficult, particularly at temperatures in the vicinity of the Oh -> C5v transformation, when starting from the C5v structure. Compared to PTMC, the hybrid algorithm is about 10 times faster for reaching equilibrium in the 1D model potential and is about 3 times faster for reaching equilibrium in the LJ38 system when starting from the second lowest energy minimum. The Wang-Landau free random walk algorithm is also applied to Ar13 and Ar38

On the relationship between thermal stability and catalytic power of enzymes

The  possible  relationship  between  the  thermal  stability  and  the  catalytic  power  of  enzymes  is  of   great  current  interest.  In  particular,  it  has  been  suggested  that  thermophilic  or  hyperthermophilic   (Tm)   enzymes   have   lower   catalytic   power   at   a   given   temperature   than   the   corresponding   mesophilic   (Ms)   enzymes,   because   the   thermophilic   enzymes   are   less   flexible   (assuming   that   flexibility   and   catalysis   are   directly   correlated).   These   suggestions   presume   that   the   reduced   dynamics   of   the   thermophilic   enzymes   is   the   reason   for   their   reduced   catalytic   power.   The   present  paper  takes  the  specific  case  of  dihydrofolate  reductase  (DHFR) and explores the validity of the above argument by simulation approaches. It is found that the Tm enzymes have restricted motions in the direction of the folding coordinate, but this is not relevant to the chemical process, since the motions along the reaction coordinate are perpendicular to the folding motions. Moreover, it is shown that the rate of the chemical reaction is determined by the activation barrier and the corresponding reorganization energy, rather than by dynamics or flexibility in the ground state. In fact, as far as flexibility is concerned, we conclude that the displacement along the reaction coordinate is larger in the Tm enzyme than in the Ms enzyme and that the general trend in enzyme catalysis is that the best catalyst involves less motion during the reaction than the less optimal catalyst. The relationship between thermal stability and catalysis appears to reflect the fact that in order to obtain small electrostatic reorganization energy it is necessary to invest some folding energy in the overall preorganization process. Thus, the optimized catalysts are less stable. This trend is clearly observed in the DHFR case

Technical Difficulties and Countermeasures of Drilling of Φ118mm Sidetracking Horizontal Well in Changqing Oilfield

The boreholes of the horizontal side-drilled wells with casing windows in Changqing Oilfield are all Φ118mm. Difficulties in the construction of small-hole drilling include high landing risk in the horizontal section, difficulty in slope prediction and trajectory control, and limited extension capacity of small wellbore. By optimizing the trajectory of the borehole, designing the trajectory adjustment section before the horizontal landing well, and introducing the equilibrium trend angle method to predict the slope of the directional tool, we improved the trajectory control ability; by calculating the stability of the drill string and the loss of cyclic pressure and analyzing the displacement extension ability, we optimized drill string selection and formed a precise trajectory control method based on sidetrack horizontal well trajectory optimization. Based on the analysis of displacement and extension ability, a non-standard drill pipe with a large diameter of 88.9mm and a small hydrophthalmia was selected. It is considered that the technical countermeasures and suggestions in this paper are of good reference and guiding significance for the development of sidetracked horizontal wells drilling in Changqing Oilfield

Transition of Cellulose Crystalline Structure and Surface Morphology of Biomass as a Function of Ionic Liquid Pretreatment and Its Relation to Enzymatic Hydrolysis

Cellulose is inherently resistant to breakdown, and the native crystalline structure (cellulose I) of cellulose is considered to be one of themajor factors limiting its potential in terms of cost-competitive lignocellulosic biofuel production. Here we report the impact of ionic liquid pretreatment on the cellulose crystalline structure in different feedstocks, including microcrystalline cellulose (Avicel), switchgrass (Panicum virgatum), pine (Pinus radiata), and eucalyptus (Eucalyptus globulus), and its influence on cellulose hydrolysis kinetics of the resultant biomass. These feedstocks were pretreated using 1-ethyl-3-methyl imidazolium acetate ([C2mim][OAc]) at 120 and 160°C for 1, 3, 6, and 12 h. The influence of the pretreatment conditions on the cellulose crystalline structure was analyzed by X-ray diffraction (XRD).On a larger length scale, the impact of ionic liquid pretreatment on the surface roughness of the biomass was determined by small-angle neutron scattering (SANS). Pretreatment resulted in a loss of native cellulose crystalline structure. However, the transformation processes were distinctly different for Avicel and for the biomass samples. For Avicel, a transformation to cellulose II occurred for all processing conditions. For the biomass samples, the data suggest that pretreatment formost conditions resulted in an expanded cellulose I lattice. For switchgrass, first evidence of cellulose II only occurred after 12 h of pretreatment at 120°C. For eucalyptus, first evidence of cellulose II required more intense pretreatment (3 h at 160°C). For pine, no clear evidence of cellulose II contentwas detected for the most intense pretreatment conditions of this study (12 h at 160°C). Interestingly, the rate of enzymatic hydrolysis of Avicel was slightly lower for pretreatment at 160°C compared with pretreatment at 120°C. For the biomass samples, the hydrolysis rate was much greater for pretreatment at 160°C compared with pretreatment at 120°C. The result for Avicel can be explained by more complete conversion to cellulose II upon precipitation after pretreatment at 160°C. By comparison, the result for the biomass samples suggests that another factor, likely lignincarbohydrate complexes, also impacts the rate of cellulose hydrolysis in addition to cellulose crystallinity

Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Cinnamomum camphora ('Gantong 1')

Cinnamomum camphora is one of the most commonly used tree species in landscaping. Improving its ornamental traits, particularly bark and leaf colors, is one of the key breeding goals. The basic helix-loop-helix (bHLH) transcription factors (TFs) are crucial in controlling anthocyanin biosynthesis in many plants. However, their role in C. camphora remains largely unknown. In this study, we identified 150 bHLH TFs (CcbHLHs) using natural mutant C. camphora 'Gantong 1', which has unusual bark and leaf colors. Phylogenetic analysis revealed that 150 CcbHLHs were divided into 26 subfamilies which shared similar gene structures and conserved motifs. According to the protein homology analysis, we identified four candidate CcbHLHs that were highly conserved compared to the TT8 protein in A. thaliana. These TFs are potentially involved in anthocyanin biosynthesis in C. camphora. RNA-seq analysis revealed specific expression patterns of CcbHLHs in different tissue types. Furthermore, we verified expression patterns of seven CcbHLHs (CcbHLH001, CcbHLH015, CcbHLH017, CcbHLH022, CcbHLH101, CcbHLH118, and CcbHLH134) in various tissue types at different growth stages using qRT-PCR. This study opens a new avenue for subsequent research on anthocyanin biosynthesis regulated by CcbHLH TFs in C. camphora

Imaging real-space flat band localization in kagome magnet FeSn

Kagome lattices host flat bands due to their frustrated lattice geometry, which leads to destructive quantum interference of electron wave functions. Here, we report imaging of the kagome flat band localization in real-space using scanning tunneling microscopy. We identify both the Fe3Sn kagome lattice layer and the Sn2 honeycomb layer with atomic resolution in kagome antiferromagnet FeSn. On the Fe3Sn lattice, at the flat band energy determined by the angle resolved photoemission spectroscopy, tunneling spectroscopy detects an unusual state localized uniquely at the Fe kagome lattice network. We further show that the vectorial in-plane magnetic field manipulates the spatial anisotropy of the localization state within each kagome unit cell. Our results are consistent with the real-space flat band localization in the magnetic kagome lattice. We further discuss the magnetic tuning of flat band localization under the spin-orbit coupled magnetic kagome lattice model.Comment: To appear in Communications Material

Proceedings of the 29th EG-ICE International Workshop on Intelligent Computing in Engineering

This publication is the Proceedings of the 29th EG-ICE International Workshop on Intelligent Computing in Engineering from July 6-8, 2022. The EG-ICE International Workshop on Intelligent Computing in Engineering brings together international experts working on the interface between advanced computing and modern engineering challenges. Many engineering tasks require open-world resolution of challenges such as supporting multi-actor collaboration, coping with approximate models, providing effective engineer-computer interaction, search in multi-dimensional solution spaces, accommodating uncertainty, including specialist domain knowledge, performing sensor-data interpretation and dealing with incomplete knowledge. While results from computer science provide much initial support for resolution, adaptation is unavoidable and most importantly, feedback from addressing engineering challenges drives fundamental computer-science research. Competence and knowledge transfer goes both ways. &nbsp

Proceedings of the 29th EG-ICE International Workshop on Intelligent Computing in Engineering

This publication is the Proceedings of the 29th EG-ICE International Workshop on Intelligent Computing in Engineering from July 6-8, 2022. The EG-ICE International Workshop on Intelligent Computing in Engineering brings together international experts working on the interface between advanced computing and modern engineering challenges. Many engineering tasks require open-world resolution of challenges such as supporting multi-actor collaboration, coping with approximate models, providing effective engineer-computer interaction, search in multi-dimensional solution spaces, accommodating uncertainty, including specialist domain knowledge, performing sensor-data interpretation and dealing with incomplete knowledge. While results from computer science provide much initial support for resolution, adaptation is unavoidable and most importantly, feedback from addressing engineering challenges drives fundamental computer-science research. Competence and knowledge transfer goes both ways. &nbsp