1,721,120 research outputs found
Molecular Dynamics Investigation of 23Na NMR Relaxation in Oligomeric DNA Aqueous Solution
No full textAn 8 ns molecular dynamics (MD) simulation has been carried out on an oligomeric DNA duplex in a minimal salt sodium aqueous solution in order to study the magnetic relaxation process of Na-23. The explicit modeling of the solvent and the time length of the simulation allow study of the fast and, to some extent, the slow components of the relaxation. In agreement with experimental studies of the quadrupolar relaxation of monatomic cations in oligomeric DNA solution, the relaxation displays a multiexponential decay. According to the simulation, the slow components originate from ions directly bound to the DNA surface. The effects of the binding of the cations to DNA on the static and dynamical relaxation parameters have been studied in different binding sites either in the grooves or in the backbone. This study reveals that the quadrupolar coupling constant and the spectral densities vary largely from site to site, the fastest relaxation occurring for the ion directly bound to the minor groove. The combination of MD results with quadrupolar relaxation experimental data suggests that the occupancy of the binding sites in the minor groove of uninterrupted adenine sequences is relatively low
Section Introduction : Molecular Dynamics Simulations and Reaction Rates
No full textThis collection about “Molecular Dynamics simulations and reaction rates” in the “Comprehensive Computational Chemistry” series has attracted excellent scholars from the entire field. Among them are many pioneers and developers of novel methods and tools. The volume features the latest developments of widely used packages to perform MD simulations, methodological advances and many ingenious applications of the state-of-the-art MD methodology, with very different types of materials in varying conditions and for systems of high complexity that could not have been simulated in the past. The contributions in this collection demonstrate the vast potential and promise of utilizing MD, the primary particle-based computer simulation method, to investigate the structural, thermodynamic, and dynamic properties of molecular matter, modeled on multiple scales from including the electronic degrees-of-freedom to meso-scale soft particles, both at equilibrium and non-equilibrium conditions. Many new ideas are given to detect rare events and to improve the poor sampling as well as to connect spatial and temporal scales in multi-scale modeling. Readers can find many ideas on where MD is going in the future, aided by the many flavors of artificial intelligence, combined with knowledge-based modeling and new sophisticated schemes allowing chemical reactions to enter into simulations having classical mechanics as foundation. With such a rapid development it would really be interesting to see in the crystal ball what we will be simulating ten years from now. In this introduction to the volume and research field, we start by looking at the rear-view mirror and discuss some selected single developments that have made the entire Computational Chemistry possible. The present and future is well covered by the contributions of excellent authors to this volume.</p
The Development of Hierarchical Ion Models and Multiscale Modeling of Tetraalkylphosphonium and Imidazolium Ionic Liquids
No full textIonic liquid (IL) materials are promising electrolytes with striking physicochemical properties for energy and environmental applications. Heterogeneous structures and transport quantities of ILs are intrinsically intercorrelated and span multiple spatiotemporal scales. Multiscale modeling methodology unifying theoretical calculations, atomistic, and coarse-grained simulations based on successive coarse-graining schemes is an efficient approach to explore complex phase behaviors of these ion-containing materials at extended spatiotemporal scales with a modest computational cost. In this chapter, we will provide several examples concentrated on tetraalkylphosphonium and imidazolium ILs showing how to sketch an effective modeling protocol to obtain force field parameters derived at high-resolution scales being transferred to low-resolution levels in a self-consistent computational scheme using a bottom-up approach bridging different length and time scales. Concluding remarks and an outlook on multiscale strategies in understanding and predictive capabilities of ILs and their mixtures are addressed in the final section to highlight future challenges and opportunities associated with IL materials in multiscale modeling community
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Hypericin, an intriguing internally heterogenous molecule, forms a covalent intramolecular hydrogen bond
No full text
- …
