We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

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The Amber biomolecular simulation programs

Chitin and chitosan: Properties and applications

This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).

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Cellulose nanomaterials review: structure, properties and nanocomposites

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.

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Microbial cellulose utilization: fundamentals and biotechnology.

A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

Modeling polysaccharides: present status and challenges.

Predicted Influence of N-Acetyl Group Content on the Conformational Extension of Chitin and Chitosan Chains

The hydration of sucrose

Conformational energy maps and descriptions of structures at the local minima are presented for the following fragments found inN-acetyllactosaminic type glycans of N-glycoproteins: GlcNAcβ(1–2)Man, GlcNAcβ(1–4)Man, GlcNAcβ(1–6)Man, Galβ(1–4)GlcNAc, GlcNAcβ(1–3)Gal, Fucα(1–6)GlcNAc, Fucα(1–3)GlcNAc, Xylβ(1–2)Man, Galβ(1–3)GlcNAc and GlcNAcβ(1–6)Gal. These results are the second part of a data bank on glycoprotein moieties; five disaccharides found in oligomannose type N-glycans were analysed earlier (Imbertyet al., 1990,Glycoconjugate J7:27–54). In the present study, three to seven minima are found for each dimer. Conformations of disaccharide fragments found in the crystal structure of the complex of a biantennary octasaccharide withLathyrus ochrus lectin are plotted on these energy maps. While the observed conformations are at predicted minima, they are not always at the minimum predicted to have the lowest energy. Further, not all observed conformations are stabilized by the exo-anomeric effect. We conclude that these oligosaccharides are highly flexible.

Data bank of three-dimensional structures of disaccharides: Part II, N-acetyllactosaminic type N-glycans. Comparison with the crystal structure of a biantennary octasaccharide.

The packing of β-1,4-glucopyranose chains has been modeled to further elaborate the molecular structures of native cellulose microfibrils. A chain pairing procedure was implemented that evaluates the optimal interchain distance and energy for all possible settings of the two chains. Starting with a rigid model of an isolated chain, its interaction with a second chain was studied at various helix-axis translations and mutual rotational orientations while keeping the chains at van der Waals separation. For each setting, the sum of the van der Waals and hydrogen-bonding energy was calculated. No energy minimization was performed during the initial screening, but the energy and interchain distances were mapped to a three-dimensional grid, with evaluation of parallel settings of the cellulose chains. The emergence of several energy minima suggests that parallel chains of cellulose can be paired in a variety of stable orientations.



A further analysis considered all possible parallel arrangements occurring between a cellulose chain pair and a further cellulose chain. Among all the low-energy three-chain models, only a few of them yield closely packed three-dimensional arrangements. From these, unit-cell dimensions as well as lattice symmetry were derived; interestingly two of them correspond closely to the observed allomorphs of crystalline native cellulose. The most favorable structural models were then optimized using a minicrystal procedure in conjunction with the MM3 force field.



The two best crystal lattice predictions were for a triclinic (P1) and a monoclinic (P21) arrangement with unit cell dimensions a = 0.63, b = 0.69, c = 1.036 nm, α = 113.0, β = 121.1, γ = 76.0°, and a = 0.87, b = 0.75, c = 1.036 nm, γ = 94.1°, respectively. They correspond closely to the respective lattice symmetry and unit-cell dimensions that have been reported for cellulose Iα and cellulose Iβ allomorphs. The suitability of the modeling protocol is endorsed by the agreement between the predicted and experimental unit-cell dimensions. The results provide pertinent information toward the construction of macromolecular models of microfibrils. © 2000 John Wiley & Sons, Inc. Biopoly 54: 342–354, 2000

Serge Pérez

Papers

Modeling polysaccharides: present status and challenges.

Predicted Influence of N-Acetyl Group Content on the Conformational Extension of Chitin and Chitosan Chains

The hydration of sucrose

Data bank of three-dimensional structures of disaccharides: Part II, N-acetyllactosaminic type N-glycans. Comparison with the crystal structure of a biantennary octasaccharide.

A priori crystal structure prediction of native celluloses.