Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures
2016
We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromo…
A step forward in disclosing the secret of stradivari's varnish by NMR spectroscopy
2017
It is commonly thought that the varnishes used by the great violin-maker Antonio Stradivari may have a role in determining not only the esthetical features but also the acoustic properties of his instruments, and the idea of a “lost secret” is still widespread among musicians and violin-makers. Previous scientific researches on varnish samples of Stradivari's instruments revealed that they were generally made by a mix of linseed oil with and colophony or metal rosinates in different ratios ranging between 75/25 (oil/resin) and 60/40 (oil/rosinate). However, it is still not clear whether the mixture composition can be related to any structural and/or functional feature of the resulting varni…
Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules
2019
We present force probe molecular dynamics simulations of dimers of interlocked calixarene nanocapsules and study the impact of structural details and solvent properties on the mechanical unfolding pathways. The system consists of two calixarene "cups" that form a catenane structure via interlocked aliphatic loops of tunable length. The dimer shows reversible rebinding, and the kinetics of the system can be understood in terms of a two-state model for shorter loops (≤14 CH2 units) and a three-state model for longer loops (≥15 CH2 units). The various conformational states of the dimer are stabilized by networks of hydrogen bonds, the mechanical susceptibility of which can be altered by changi…
Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies
2013
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water cluste…
In Silico Design Enables the Rapid Production of Surface-Active Colloidal Amphiphiles
2020
A new technology platform built on the integration of theory and experiments to enable the design of Janus colloids with precision control of surface anisotropy and amphiphilicity could lead to a disruptive transformation in the next generation of surfactants, photonic or phononic materials, and coatings. Here, we exploit molecular dynamics (MD) simulations to guide the rational design of amphiphilic polymer Janus colloids by Flash NanoPrecipitation (FNP), a method capable of the production of colloids with complex structure without the compromise of reduced scalability. Aided by in silico design, we show in experiments that amphiphilic Janus colloids can be produced using a unique blend of…
Interfacial Domain Formation Enhances Electrochemical Synthesis.
2019
The electroorganic C,C coupling of phenols to other aryl components is controlled by the fluoroalcohol-alcohol mixture solvents. Classical molecular dynamics and static density functional theory reveal that both kinds of solvents interact with the substrates, influencing the electronic structure of a phenoxyl radical intermediate in a cooperative manner to achieve maximal efficiency and selectivity. Simulations of the electrolyte-electrode interface showed that the substrates adsorb on the diamond surface in such a way that the repulsive fluorous-lipophilic interactions can be minimized and the attractive lipophilic-lipophilic interplay can be maximized, whereas the advantageous hydrogen bo…
The Surface of Ice under Equilibrium and Nonequilibrium Conditions
2019
ConspectusThe ice premelt, often called the quasi-liquid layer (QLL), is key for the lubrication of ice, gas uptake by ice, and growth of aerosols. Despite its apparent importance, in-depth understanding of the ice premelt from the microscopic to the macroscopic scale has not been gained. By reviewing data obtained using molecular dynamics (MD) simulations, sum-frequency generation (SFG) spectroscopy, and laser confocal differential interference contrast microscopy (LCM-DIM), we provide a unified view of the experimentally observed variation in quasi-liquid (QL) states. In particular, we disentangle three distinct types of QL states of disordered layers, QL-droplet, and QL-film and discuss…
Theoretical Study on the Diffusion Mechanism of Cd in the Cu-Poor Phase of CuInSe2 Solar Cell Material
2013
We have employed first-principles static and molecular dynamics (MD) calculations with semilocal and screened-exchange hybrid density functionals to study the diffusion of Cd in bulk CuIn5Se8, a copper-poor ordered vacancy compound of CuInSe2. The diffusion mechanism and the underlying kinetics/energetics were investigated by combining ab initio metadynamics simulations and nudged elastic band (NEB) calculations. We found that the migration of Cd occurs via a kick-out of Cu atoms, assisted by the pristine vacancies that are constitutive of this compound, and follows a double-hump energy profile. The rate-limiting step has a barrier of about 1 eV at 0 K but reduces to 0.3 eV at 850 K, pointi…
Photoelectron spectra of aluminum cluster anions: Temperature effects and ab initio simulations
1999
Photoelectron (PES) spectra from aluminum cluster anions (from 12 to 15 atoms) at various temperature regimes, were studied using ab-initio molecular dynamics simulations and experimentally. The calculated PES spectra, obtained via shifting of the simulated electronic densities of states by the self-consistently determined values of the asymptotic exchange-correlation potential, agree well with the measured ones, allowing reliable structural assignments and theoretical estimation of the clusters' temperatures.
Treatment of disorder effects in X-ray absorption spectra beyond the conventional approach
2020
The contribution of static and thermal disorder is one of the largest challenges for the accurate determination of the atomic structure from the extended X-ray absorption fine structure (EXAFS). Although there are a number of generally accepted approaches to solve this problem, which are widely used in the EXAFS data analysis, they often provide less accurate results when applied to outer coordination shells around the absorbing atom. In this case, the advanced techniques based on the molecular dynamics and reverse Monte Carlo simulations are known to be more appropriate: their strengths and weaknesses are reviewed here.