Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and ...electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques in order that readers can understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely-used Car-Parrinello approach, correcting various misconceptions currently found in research literature. The book also contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly-used program packages, and enabling developers to improve and add new features in their code. • Discusses the Car-Parrinello approach and its special features helping to correct various misconceptions currently found in research literature • Allows readers to understand widely used program packages and to improve their own programs by featuring pseudo-code and program layout • Enables readers to assess the pros and cons of commonly used ab initio simulation methods by including systematic derivations of ab initio molecular dynamics schemes
The relationship between structure and reactivity plays a dominant role in water dissociation on the various TiOsub.2 crystallines. To observe the adsorption and dissociation behavior of Hsub.2O, the ...reaction force field (ReaxFF) is used to investigate the dynamic behavior of Hsub.2O on rutile (110) and anatase (101) surfaces in an aqueous environment. Simulation results show that there is a direct proton transfer between the adsorbed Hsub.2O (Hsub.2Osub.ad) and the bridging oxygen (Osub.br) on the rutile (110) surface. Compared with that on the rutile (110) surface, an indirect proton transfer occurs on the anatase (101) surface along the H-bond network from the second layer of water. This different mechanism of water dissociation is determined by the distance between the 5-fold coordinated Ti (Tisub.5c) and Osub.br of the rutile and anatase TiOsub.2 surfaces, resulting in the direct or indirect proton transfer. Additionally, the hydrogen bond (H-bond) network plays a crucial role in the adsorption and dissociation of Hsub.2O on the TiOsub.2 surface. To describe interfacial water structures between TiOsub.2 and bulk water, the double-layer model is proposed. The first layer is the dissociated Hsub.2O on the rutile (110) and anatase (101) surfaces. The second layer forms an ordered water structure adsorbed to the surface Osub.br or terminal OH group through strong hydrogen bonding (H-bonding). Affected by the H-bond network, the Hsub.2O dissociation on the rutile (110) surface is inhibited but that on the anatase (101) surface is promoted.
Featured Cover Vlassis, Nikolaos N.; Zhao, Puhan; Ma, Ran ...
International journal for numerical methods in engineering,
09/2022, Letnik:
123, Številka:
17
Journal Article
Recenzirano
Odprti dostop
The cover image is based on the Original Article Molecular dynamics inferred transfer learning models for finite‐strain hyperelasticity of monoclinic crystals: Sobolev training and validations ...against physical constraints by Nikolaos Vlassis et al., https://doi.org/10.1002/nme.6992.
The inclusion complexes of cucurbitnuril, CBn (n = 6–8), with poly aromatic hydrocarbon (PAH) Benzo(a)Pyrene (BaP), and fluoranthene (FLT) were investigated carefully in aqueous media. Fluorescence ...and sup.1H NMR spectroscopy were used to characterize and investigate the inclusion complexes that were prepared in the aqueous media. The most predominant complexes of both guests with hosts were the 1:1 guest: host complexes. Stability constants of 2322 ± 547 Msup.−1, 7281 ± 689 Msup.−1, 3566 ± 473 Msup.−1 were obtained for the complexes of BaP with CB6, CB7, and CB8, respectively. On the other hand, stability constants of 5900.270 ± 326 Msup.−1, 726.87 ± 78 Msup.−1, 3327.059 ± 153 Msup.−1 were obtained for the complexes of FLT with CB6, CB7, and CB8, respectively. Molecular dynamic (MD) simulations were used to study the mode and mechanism of the inclusion process and to monitor the stability of these complexes in aqueous media at an atomistic level. Analysis of MD trajectories has shown that both BaP and FLT form stable inclusion complexes with CB7 and CB8 in aqueous media throughout the simulation time, subsequently corroborating the experimental results. Nevertheless, the small size of CB6 prohibited the encapsulation of the two PAHs inside the cavity, but stable exclusion complex was observed between them. The main driving forces for the stability of these complexes are the hydrophobic forces, van der Waals interactions, electrostatic effect, the π····π and C–H···π interaction. These results suggest that BaP and FLT can form stable complexes with CBn (n = 6–8) in solution.
How to fabricate large area controllable surface-enhanced Raman scattering (SERS) active nanostructure substrates has always been one of the important issues in the development of nanostructure ...devices. In this paper, nano-etching technology and magnetron sputtering technology are combined to prepare nanostructure substrate with evolvable structure, and Ag/TiOsub.2/Ag composites are introduced into the evolvable composite structure. The activity of SERS is further enhanced by the combination of TiOsub.2 and Ag and the electron transfer characteristics of TiOsub.2 itself. Deposition, plasma etching, and transfer are carried out on self-assembled 200 nm polystyrene (PS) colloidal sphere arrays. Due to the shadow effect between colloidal spheres and the size of metal particles introduced by deposition, a series of Ag/TiOsub.2/Ag nanostructure arrays with adjustable nanostructure substrates such as nano-cap (NC), nano cap-star (NCS), and nano particle-disk (NPD) can be obtained. These nanoarrays with rough surfaces and different evolutionary structures can uninterruptedly regulate optical plasmon resonance and reconstruct SERS hotspots over a large range, which has potential application value in surface science, chemical detection, nanometer photonics, and so on.
The results of dielectric relaxation spectroscopy of the chiral liquid crystal 4′-butyl-4-(2-methylbutoxy)azoxybenzene in the crystal phase are presented. The scaling procedure showed complex ...molecular dynamics and allows one to decompose the observed relaxation process into two closely located relaxation processes around the short molecular axis. Temperature dependences of relaxation times characterizing flip-flop motions (rotation around the short molecular axis) and rotation around the long molecular axis are of the Arrhenius type.
Micro-Exon Genes are a widespread class of genes known for their high variability, widespread in the genome of parasitic trematodes such as Schistosoma mansoni. In this study, we present a strategy ...that allowed us to solve the structures of three alternatively spliced isoforms from the Schistoma mansoni MEG 2.1 family for the first time. All isoforms are hydrophobic, intrinsically disordered, and recalcitrant to be expressed in high yield in heterologous hosts. We resorted to the chemical synthesis of shorter pieces, before reconstructing the entire sequence. Here, we show that isoform 1 partially folds in a-helix in the presence of trifluoroethanol while isoform 2 features two rigid elbows, that maintain the peptide as disordered, preventing any structuring. Finally, isoform 3 is dominated by the signal peptide, which folds into a-helix. We demonstrated that combining biophysical techniques, like circular dichroism and nuclear magnetic resonance at natural abundance, with in silico molecular dynamics simulation for isoform 1 only, was the key to solve the structure of MEG 2.1. Our results provide a crucial piece to the puzzle of this elusive and highly variable class of proteins.
This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular ...dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs E(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging and diverse set of molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.