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Atomistic molecular dynamics simulations were carried out to obtain information on the rheological, aggregation and disintegration properties of carboxylated (TEMPO-oxidized) cellulose nanofibrils with different functionalization levels. The magnitude of the inter-fibril interaction was quantified for parallel nanofibrils using the umbrella sampling method. The obtained potential of mean force was found highly sensitive to the charge configuration for intermediate functionalization levels. This feature was further studied with an electrostatic model for similar charge configurations and system periodicity as in the case of the molecular dynamics simulations. The electrostatic contribution of the charged surfaces varied from repulsive to attractive depending on the distribution of the carboxylate groups and nearby counter-ions, as well as the distance between the fibrils. The simulated deviations from average behavior for single fibrils in both models suggest heterogeneity in their aggregation and disintegration behavior. This was seen in disintegration experiments, where the differences in disintegration energy and in the structural variation qualitatively agreed with the model predictions. As to aggregation behavior, the studied case with parallel fibrils reflects the upper boundary of the repulsive interaction.

We uncover the electronic structure of molecular graphene produced by adsorbed CO molecules on a copper (111) surface by means of first-principles calculations. Our results show that the band structure is fundamentally different from that of conventional graphene, and the unique features of the electronic states arise from coexisting honeycomb and Kagome symmetries. Furthermore, the Dirac cone does not appear at the K-point but at the Γ-point in the reciprocal space and is accompanied by a third, almost flat band. Calculations of the surface structure with Kekule distortion show a gap opening at the Dirac point in agreement with experiments. Simple tight-binding models are used to support the first-principles results and to explain the physical characteristics behind the electronic band structures.

We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril.

The formation of extended electron states in one-dimensional nanostructures is of key importance for the function of molecular electronics devices. Here we study the effects of strong electron-phonon interaction on the formation of extended electronic states in intentionally created Cl vacancy pairs and chains in a NaCl bilayer on Cu(111). The interaction between the vacancies was tailored by fabricating vacancy pairs and chains of different orientation and separation with atomic precision using vertical manipulation. Small separation of divacancies led to the formation of symmetric and antisymmetric vacancy states and localized interface-states. By scanning tunneling spectroscopy (STS) we measured their energy splitting and broadening as a function of the inter-vacancy separation. Unexpectedly, the energy splitting between the vacancy states is enlarged by level repulsion resulting from phonon dressing of the electronic states, as evidenced by theory. Already for a few coupled vacancies we observe an emerging band structure of the defect band., 9 pages, 4 figures

Transformation of cellulose into monosaccharides can be achieved in a chemical process performed by a special group of enzymes known as cellulases. We have used atomistic molecular dynamics simulations to study endoglucanase II (Cel5A) that is one of the proteins in this group. Based on the atomistic simulation results, we discuss how the Cel5A enzyme interacts with cellulose fibrils comprised of both crystalline and amorphous regions. We show that the enzyme’s carbohydrate-binding domain prefers to interact with crystalline regions of cellulose, while the catalytic domain has a high affinity to the amorphous regions of fibrils. In particular, through electrostatic interactions the catalytic domain attracts loose glucose chains to its catalytic cleft. The atomistic details of the enzyme–cellulose interaction are presented and the implications for practical applications are briefly discussed.

Man-made artificial graphene has attracted significant attention in the past few years due to the possibilities to construct designer Dirac fermions with unexpected topological properties and applications in nanoelectronics. Here we use a first-principles approach within density-functional theory to study molecular graphene similar to the experiment by Gomes~{\em et al.}, Nature {\bf 483}, 306 (2012). The system comprises carbon monoxide molecules arranged on a copper (111) surface in such a way that a hexagonal lattice is obtained with the characteristic electronic properties of graphene. Our results show in detail how carbon monoxide molecules modify the copper surface (and regions beneath) and create a hexagonal lattice of accumulated electrons between the adsorbate molecules. We also demonstrate how the properties of the formed Dirac fermions change as the CO density is tuned, and provide a direct comparison with experimental scanning tunneling microscope images.

A combined study using density functional calculations and scanning tunneling microscopy experiments shows that individual silver adatoms on ultrathin sodium chloride films on copper surfaces are stable in three different charge states—neutral, negatively, and positively charged adatoms. The charge states of the individual adatoms were manipulated by voltage pulses. The key parameters determining the stability of various charge states are identified and discussed within a simple model.

Broad Gaussian line shapes are observed in scanning tunneling spectroscopy of single, localized electronic states induced by Cl vacancies in ultrathin NaCl films on Cu surfaces. Using a simple inelastic resonance tunneling model, we show that the observed broad line shapes are caused by a strong coupling between the localized state and the optical phonons in the film. The parameters for the model are obtained from density functional calculations, in which the occupation of the vacancy state temporarily taking place in the experiment has also been accounted for.