Monte Carlo and molecular dynamics simulations were performed to investigate the effect on the solubility, diffusion, and permeability of water and oxygen when adding graphene or single-walled carbon nanotubes (SWCNTs) to polyethylene (PE). When compared with pure PE, addition of graphene lowered the solubility of water, whereas at lower temperatures, the oxygen solubility increased because of the oxygen–graphene interaction. Addition of SWCNTs lowered the solubility of both water and oxygen when compared with pure PE. A detailed analysis showed that an ordered structure of PE is induced near the additive surface, which leads to a decrease in the diffusion coefficient of both penetrants in this region. The addition of graphene does not change the permeation coefficient of oxygen (in the direction parallel to the filler) and, in fact, may even increase this coefficient when compared with pure PE. In contrast, the water permeability is decreased when graphene is added to PE. The addition of SWCNTs decreases the permeability of both penetrants. Graphene can consequently be added to selectively increase the solubility and permeation of oxygen over water, at least at lower temperatures. 

Monte Carlo and molecular dynamics simulations were performed to calculate solubility, S, and diffusion, D, coefficients of oxygen and water in polyethylene, and to obtain a molecular-level understanding of the diffusion mechanism. The permeation coefficient, P, was calculated from the product of S and D. The AMBER force field, which yields the correct polymer densities under the conditions studied, was used for the simulations, and it was observed that the results were not sensitive to the inclusion of atomic charges in the force field. The simulated S for oxygen and water are higher and lower than experimental data, respectively. The calculated diffusion coefficients are in good agreement with experimental data. Possible reasons for the discrepancy in the simulated and experimental solubilities, which results in discrepancies in the permeation coefficients, are discussed. The diffusion of both penetrants occurs mainly by large amplitude, infrequent jumps of the molecules through the polymer matrix.

Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation and cyclization of two 5-aminolevulinic acid (5-ALA) substrate molecules to give porphobilinogen (PBG). The chemical step of PBGS is herein revisited using QM/MM (ONIOM) calculations. Two different protonation states and several different mechanisms are considered. Previous mechanisms based on DFT-only calculations are shown unlikely to occur. According to these new calculations, the deprotonation step rather than ring closure is rate-limiting. Both the C–C bond formation first mechanism and the C–N bond formation first mechanism are possible, depending on how the A-site ALA binds to the enzyme. We furthermore propose that future work should focus on the substrate binding step rather than the enzymatic mechanism.

Molecular dynamics (MD) simulations have been used to study the melting of α- and β-poly (vinylidene fluoride) (α- and β-PVDF). It is seen that melting at the ends of the polymer chains precedes melting of the bulk crystal structure. Melting of α-PVDF initially occurs via transitions between the two gauche dihedral angles (G ↔ G′) followed by transitions between trans and gauche dihedral angles (T ↔ G/G′). Melting of β-PVDF initially occurs via T → G/G′ transitions and via transitions of complete β- (TTTT) to α- (TGTG') quartets. The melting point of β-PVDF is higher than that of α-PVDF, and the simulated melting points of both phases depend on the length of the polymer chains used in the simulations. Since melting starts at the chain ends, it is important to include these in the simulations, and simulations of infinitely long chains yield melting points far larger than the experimental values (at least for periodic cells of the size used in this work), especially for β-PVDF. The simulated heats of fusion are in agreement with available experimental data.

Hydrogels are used for various applications, for example as transporters in drug delivery, in control lenses, and as superabsorbent material in diapers.[1] Most synthetic produced hydrogels are based on synthetic polymers. Even though they are efficient and cheap, they are not biodegradable and sometimes even toxic. To produce more environmental friendly and biodegradable superabsorbent polymers (Bio- SAPs), other building blocks can be used, such as polysaccharides[2] and various protein structures, for example fish shells[3], collagen[4], soy protein[5] and egg protein[6]. Experimental studies at the University of Boras show that it is possible to produce Bio-SAPs from by-products of ethanol production from ligno-cellulose.[2, 6, 7] 2. Method We have studied the absorption properties of protein structures in silico as a comparison to experimental studies. The NPT Gibbs Ensemble Monte Carlo (GEMC) simulation scheme with two phases is used in order to calculate the absorption capacity of the protein. Pure water was simulated in the first GEMC-phase and the peptide in the second phase. The simulations were made with SPC/E water model [8] and the AMBER99 atomistic force field for the peptides [9]. Furthermore, mesoscopic studies with coarse grained force fields have been done. To facilitate faster computations, we used cell lists for the atom-atom interactions, configurational bias algorithm to build the water molecules and the peptide side-chains, and the cavity bias algorithm [10] for molecule insertions. Model peptides have been studied with varying secondary structure, temperature and protonation (pH). We also plan to study how cross-links affect the absorption. One of the peptides we study is a 20 amino acid long peptide called SSP1.[11] This peptide is designed to form a fibrous structure a hydrogel, and its structure is well defined. We have also studied a peptide which changes secondary structure when changing the pH, and concentration.[12] This makes it possible to compare absorption properties with respect to the secondary structure. 3. Conclusion We have simulated peptides with the Gibbs Ensemble Monte Carlo scheme in order to study the water absorption rate dependent of structure, charge, pH and temperature. This information is useful when developing new biodegradable superabsorbent materials.

Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however, is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogen synthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for the formation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to 14.0 kcal mol(-1). We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.