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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 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.

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.

We study tip-adsorbate–substrate interactions in scanning tunneling microscopy (STM) manipulation and imaging, and the influence of impurities on the images. Thence, we perform molecular dynamics simulations and calculate qualitative STM images for oxygen on Pt(1 1 1) surface. The adsorption site of the oxygen molecule is found to be in accordance with ab initio calculations. The calculated STM image has a good resemblance to the experimental ones. The contamination of the tip by oxygen or water alters the STM image strongly. Molecular dynamics simulations on manipulations of oxygen on the surface reveal several mechanisms of how molecular oxygen can be either produced or decomposed with STM tip. Finally, we find out that transfer of oxygen from the surface to an STM tip is not very probable.

Molecular dynamics simulations are performed to study adsorption of methane on Pd(1 1 0). The direct dissociation is found to take place due to transfer of incident translational energy into vibrational modes of the molecule. The deformation modes of the molecule appear to be the most susceptive to this energy transfer. At high incident translational energies the molecules tend to dissociate directly, while at intermediate energies the molecules are bounced off the surface. At low energies, the molecules are trapped into a physisorption state, which may be a gateway to thermally assisted dissociation within a longer time.

Dissociative adsorption of methane has been investigated on Pd {1 1 0} by using molecular beam surface scattering. The initial sticking probability has been determined in the translational energy range of 7–95 kJ/mol and at selected vibrational energies from 300 to 700 K. The measured initial sticking probability is found to increase strongly with both translational and vibrational energy of CH4 molecules. The activation of the dissociative chemisorption of CH4 induced by the vibrational energy is shown to depend on the translational energy and is attributed to the excitation of the bending modes of the incident molecule. We have also performed molecular dynamics simulations to investigate the dissociation mechanism theoretically. The simulations clearly demonstrate that an efficient energy transfer occurs upon adsorption between the translational and vibrational energies of the incident CH4 molecule, which thereby facilitates the deformation of the molecular structure of CH4 resulting in dissociation.

A method to calculate local electronic structure and interatomic forces for molecular dynamics simulation of a materials system with two size scales, is described. In the method, the interactions for the larger scale subsystem are modeled with semiempirical potentials, and the interactions for the smaller scale subsystem are calculated quantum mechanically. Interatomic Hellman-Feynman forces can be calculated using the off-diagonal matrix elements of density matrix derived from Green's function and the gradients of the matrix elements of the tight-binding Hamiltonian matrix. The elements of Green's function for semiempirical particles are modeled in some simple predefined form, while Green's function for the rest of the particles is calculated in tight-binding basis using Dyson's equation. As an example, dissociative adsorption of ${\mathrm{O}}_{2}$ on a stepped $\mathrm{Pd}{110}$ surface is simulated.

Dissociation of methane on $\mathrm{Pd}(110)$ and $\mathrm{Pd}(320)$ is investigated using molecular dynamics simulations and statistical analysis of excitations of vibrational modes of the molecule. Simulations are made by varying translational energy and excitations of vibrational stretching $({\ensuremath{\nu}}_{1})$ and bending $({\ensuremath{\nu}}_{2})$ modes of methane. The role of these factors in dissociation is found to depend on the adsorption path in a rather complicated way. Especially, different vibrational modes seem to facilitate dissociation at different adsorption site and for different orientation of the molecule. Statistical analysis of excitations of vibrational modes indicate that dissociation is governed at low vibrational temperatures by bending modes and on higher temperatures by stretching mode. Translational energy is still found to be more efficient activator of dissociation than vibrational energy.

We perform a molecular dynamics (MD) study of non-dissociative adsorption of O 2 molecule on Pt{111} surface at low temperatures, and analyse the STM image of the obtained geometry. The interatomic forces for the simulation are calculated using tight-binding method in density matrix formalism with the constraint of local charge neutrality. The STM image is constructed by calculating tunneling current between a sharp metal tip and the sample. The MD simulation gives an adsorption site with a very plausible bonding behaviour. Furthermore, the corresponding STM image is similar to recent experimental images. The present simulation suggests formation of a larger complex of the oxygen molecule and two Pt atoms. It turns out that the STM image does not directly show the orientation of the O 2 molecule, and has such a complicated origin in interference of atomic orbitals of the formed complex, that an optimization of the surface structure using MD simulation, instead of intuitive considerations, is necessary.