A review on systematic study of cellulose

Fine-Grained Parallel and Distributed Spatial Stochastic Simulation of Biological Reactions

Large and complex systems from the EMC point of view are objects that contain different structures requiring individually composed methods for modeling as well as calculation. Automobiles, aircraft, or PCBs with devices are large and complex systems. The paper describes activities that were done to handle automotive EMC problems with computer simulations. A set of methods was compiled to allow, in a first stage, a fast calculation model generation, and, to apply in a second stage with minimum user interaction, accurate and fast multi step hybrid methods. The paper focuses less on the methods themselves, but more on the completeness of the process chain that is required to do successful simulations of automobiles or other large systems.

Current simulation tools for multibody dynamics are not problem dependent, they use the same modeling process to all cases regardless of their characteristics. In addition, real-time simulation of small multibody systems is achievable by existing simulation tools, however, real-time simulation of large and complex systems is not possible with existing methods. This is a challenge that needs to be addressed before further advances in mechanical simulation with hardware-in-the-loop and man-in-the-loop, as well as virtual prototyping are made possible. This paper addresses the issue of how the modeling process-dependent versus independent coordinates, and descriptor form versus state-space form of the equations of motion-affects the dynamic simulation of multibody systems and how it may be taken into account and added to the concept of intelligent simulation. With this new concept all the factors involved in the simulation process — modeling, equations, solution, etc. — are chosen and combined depending upon the characteristics of the system to be simulated. It is envisioned that this concept will lead to faster and more robust real-time simulators.

The crystalline structure of native cellulose, with its unique microfibrillar morphology resulting from a complex biogenesis mechanism, has not only been the most studied subject in polymer science, but is still generating great interest along with lively debates and controversies. This issue of Cellulose features such a debate in the form of two articles dealing with the conformational analysis of the glucosidic bond in the cellulose chains. This debate is but the latest incident in a long string of events, which represent the foundation of our current understanding of this important material. This makes this an opportune moment to reflect on some of the major milestones in the history of cellulose structure evaluation, which also often involved debates and controversies. It was in 1913, i.e. close to one century ago, that Nishikawa and Ono showed the first diffraction patterns of two cellulose-based plant materials, namely bamboo and hemp, taking advantage of the discovery of the interference phenomena of X-rays reported 1 year earlier by Laue, Friedrich and Knipping. Following this early report, diffraction diagrams of a large number of cellulose materials were duly recorded and subjected to analysis, as it was felt that the knowledge of the crystalline structure of cellulose was of great importance for the development and improvement of cellulose-based products. While recording diffraction patterns of these specimens, it was soon realized that even the X-ray data sets of the most crystalline samples remained limited and it was therefore hard to deduce from them alone the required structural details. It is only when the diffraction data could be complemented by the occurrence of new techniques that substantial advances toward the structural description of cellulose could be made. The sequential emergence of such techniques explains the succession of steps leading to the present understanding. In the progress toward the molecular description of the crystal structure of cellulose from X-ray diffraction data, a first landmark was the incorporation of the stereochemistry of the glucosyl moieties in the molecular models built by, among others, Meyer and Mark (1928), later revised by Meyer and Misch (1937), who presented a model where the crystal of cellulose consisted of two antiparallel chains. This last model, which remained the established standard for at least two decades, was confronted with a series of conflicting data, resulting from new techniques. In 1958, the recording of electron diffraction diagrams of frozen Valonia cell wall fragments allowed Honjo and Watanabe to obtain diffraction data sets far better H. Chanzy—affiliated with the Universite Joseph Fourier and member of the Institut de Chimie Moleculaire de Grenoble.

Internal structure and dynamics of commercial and natural cellulose were studied by measuring chemical shift anisotropy (CSA) parameters, and spin-lattice relaxation rate (1/T1) at each and every chemically different carbon nuclear site. CSA parameters were measured by 13C two-dimensional phase adjusted spinning sideband (2DPASS) cross-polarization magic angle spinning (CP-MAS) NMR experiment. Site specific spin-lattice relaxation time was measured by Torchia-CP method. Anisotropy parameters of C4 and C6 regions are higher than C1 and C235 regions and asymmetry of C4 line is lower than any other carbon site. The higher values of CSA parameters of C4 and C6 nuclei arise due to the rotation of O4-C4, C1-O4, O5-C5-C6-O6 and C4-C5-C6-O6 bonds at torsion angles ψ, Φ, χ and χ' respectively and the influence of interchain and intrachain hydrogen bondings. Two distinct peaks are also observed for C4 and C6 resonance line position-one peak arises primarily due to the nuclei in amorphous region and another one arises due to the same nuclei resides in paracrystalline region. The spin-lattice relaxation time and the CSA parameters are different at these two distinct peak positions of C4 and C6 line. Molecular correlation time of each and every chemically different carbon site was calculated with the help of CSA parameters and spin-lattice relaxation time. The molecular correlation time of the amorphous region is one order of magnitude less than the crystalline region. The distinction between amorphous and paracrystalline regions of cellulose is more vividly portrayed by determining spin-lattice relaxation time, CSA parameters, and molecular correlation time at each and every chemically different carbon site. This type of study correlating the structure and dynamics of cellulose will illuminate the path of inventing biomimetic materials.

A theoretical model based on the competition between hydrogen-bonding energy and strain energy was constructed to explain the size of native cellulose Iβ. The cellodextrins in native crystalline cellulose Iα and Iβ are unusually stable compared to other polysaccharides, not easily prone to hydrolysis even though they are only nanometers in diameter. The stability of crystalline cellulose Iβ is most likely due to its greatly enhanced hydrogen-bonding (HB) network. We carried out ab initio calculations to determine the native crystalline cellulose Iβ atomic and conformational structures. For crystalline cellulose, we found that every hydroxyl group in the cellulose structure is hydrogen bonded as both a donor and an acceptor. This agrees well with published X-ray and neutron diffraction data. We also determined the electronic structures and the energetics for one cellodextrin chain, one to four sheets of cellodextrins in cellulose, and the bulk cellulose Iβ.

This paper documents a practical numerical method of evaluating damping of slow oscillations in computer simulations of large power systems. This technique has been tested and improved over the last two years. The damping coefficients can assist in evaluation of acceptable transfer limitations. The proposed method also provides a means to evaluate the sensitivity of various transfer path loadings and transmission and generation facility contingencies on system damping.

For efficient simulation of chemical systems with large number ofreactions, we report a fast and exact algorithm for direct simulation ofchemical discrete Markov processes. The approach adopts the scheme oforganizing the reactions into hierarchical groups. By generating arandom number, the selection of the next reaction that actually occursis accomplished by a few successive selections in the hierarchicalgroups. The algorithm which is suited for simulating systems with largenumber of reactions is much faster than the direct method or theoptimized direct method. For a demonstration of its efficiency, theaccelerated algorithm is applied to simulate the reaction-diffusionBrusselator model on a discretized space.

This study examines the performance of integration methods for hybrid simulation of large and complex structural systems in the context of structural collapse due to seismic excitations. The target application is not necessarily for real-time testing, but rather for models that involve large-scale physical sub-structures and highly nonlinear numerical models. Four case studies are presented and discussed. In the first case study, the accuracy of integration schemes including two widely used methods, namely, modified version of the implicit Newmark with fixed-number of iteration (iterative) and the operator-splitting (non-iterative) is examined through pure numerical simulations. The second case study presents the results of 10 hybrid simulations repeated with the two aforementioned integration methods considering various time steps and fixed-number of iterations for the iterative integration method. The physical sub-structure in these tests consists of a single-degree-of-freedom (SDOF) cantilever column with replaceable steel coupons that provides repeatable highlynonlinear behavior including fracture-type strength and stiffness degradations. In case study three, the implicit Newmark with fixed-number of iterations is applied for hybrid simulations of a 1:2 scale steel moment frame that includes a relatively complex nonlinear numerical substructure. Lastly, a more complex numerical substructure is considered by constructing a nonlinear computational model of a moment frame coupled to a hybrid model of a 1:2 scale steel gravity frame. The last two case studies are conducted on the same porotype structure and the selection of time steps and fixed number of iterations are closely examined in pre-test simulations. The generated unbalance forces is used as an index to track the equilibrium error and predict the accuracy and stability of the simulations.

This paper documents a practical numerical method of evaluating damping of slow oscillations in computer simulations of large power systems. This technique has been tested and improved over the last two years. The damping coefficients can assist in evaluation of acceptable transfer limitations. The proposed method also provides a means to evaluate the sensitivity of various transfer path loadings and transmission and generation facility contingencies on system damping.

The scalability of massively parallel algorithms is a fundamental question in computer science. We study the scalability and the efficiency of a conservative massively parallel algorithm for discrete-event simulations where the discrete events are Poisson arrivals. The parallel algorithm is applicable to a wide range of problems, including dynamic Monte Carlo simulations for large asynchronous systems with short-range interactions. The evolution of the simulated time horizon is analogous to a growing and fluctuating surface, and the efficiency of the algorithm corresponds to the density of local minima of this surface. In one dimension we find that the steady state of the macroscopic landscape is governed by the Edwards-Wilkinson Hamiltonian, which implies that the algorithm is scalable. Preliminary results for higher-dimensional logical topologies are discussed.

Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.

The research is aimed at solving the problem of faster than real time distributed interactive simulation for large scale systems based on personal computer networks or workstation networks. The HLA services are integrated with the reflective memory networks and the sector minimization method are used in the study. An approach is proposed to solve the problem of faster than real time data transfer, ensuring the general speed of simulation and the speed of instantaneous synchronization for the large scale system simulation. A platform based on this approach provides interface services of which the call methods are the same as HLA. Using the platform, the existing HLA simulation systems can be conveniently migrated and new simulation systems can be developed and run in faster than real time.

A parallel implementation of the Stokesian Dynamics method applied to the simulation of colloidal suspensions

In the context of a research project with the aim of investigating the influence of human-machine interfaces on the error-proneness of situation assessment in technical systems by humans, extensive user experiments have been conducted. The paper reports influences of a pattern oriented display (the mass data display) as well as time oriented displays (trend graphs) on the classification of process states. All interfaces that have been investigated were based on P&I (piping and instrumentation) diagrams, a threshold oriented visualisation form, which is commonly used in simulation and control (S&C) of large technical systems. Comparing the different displays with each other a strategy of adding and removing was applied. Primarily, the features of investigated displays are introduced and discussed. Based on the features of displays the assumed performance of each display is shown. Finally, the assumed and measured performances are compared with each other. The results are discussed as well in a taxonomy context.