Search results for " molecular dynamics"
showing 10 items of 126 documents
Ab initio molecular dynamics simulations of negative thermal expansion in ScF3: the effect of the supercell size
2020
The authors sincerely thank S. Ali, A. Kalinko, and F. Rocca for providing experimental EXAFS data, as well as M. Isupova, V. Kashcheyevs, and A. I. Popov for stimulating discussions. Financial support provided by project No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001) under the activity “Post-doctoral research aid” realized at the Institute of Solid State Physics, University of Latvia is greatly acknowledged by D.B. A.K and J.P. would like to thank the support of the Latvian Council of Science project No. lzp-2018/2–0353.
Molecular structure and multi-body potential of mean force in silica-polystyrene nanocomposites
2018
We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano et al, J. Chem. Phys. 2009, 130, 214106] to study interfacial properties and potential of mean force (PMF) for separating nanoparticles (NPs) in a melt. Specifically, we consider Silica NPs bare or grafted with Polystyrene chains, aiming to shed light on the interactions among free and grafted chains affecting the dispersion of NPs in the nanocomposite. The proposed hybrid models show good performances in catching the local structure of the chains, and in particular their density profiles, documenting the existence of the "wet-brush-to-dry-brush" transition. By using these models, the PMF b…
Melting and multipole deformation of sodium clusters
1999
Melting and multipole deformations of sodium clusters with up to 55 atoms are studied using an ab initio molecular dynamics method. The melting temperature regions for Na20, Na40, and Na 55 + are estimated. The melting temperature region determined here for Na 55 + agrees with the one determined experimentally. The dominating deformation type observed at the liquid phase for Na20 and Na40 is octupole deformation and for Na14 and Na 55 + quadrupole deformation.
Quaternary structures of GroEL and naïve-Hsp60 chaperonins in solution: a combined SAXS-MD study
2015
The quaternary structures of bacterial GroEL and human naïve-Hsp60 chaperonins in physiological conditions have been investigated by an innovative approach based on a combination of synchrotron Small Angle X-ray Scattering (SAXS) in-solution experiments and molecular dynamics (MD) simulations. Low-resolution SAXS experiments over large and highly symmetric oligomers are analyzed on the basis of the high-resolution structure of the asymmetric protein monomers, provided by MD. The results reveal remarkable differences between the solution and the crystallographic structure of GroEL and between the solution structures of GroEL and of its human homologue Hsp60.
Structure of anisole derivatives by total neutron and X-ray scattering: Evidences of weak C–H⋯O and C–H⋯π interactions in the liquid state
2020
Abstract High resolution, total neutron and X-ray scattering data have been used in synergy with Molecular Dynamics simulations to access atomistic scale insight into the structure of anisole and 2,3,5-trimethylanisole, two aromatic compounds bearing an electron-donating methoxy group. A detailed description is provided for the main interactions occurring in these systems, including π-π stacking and weak hydrogen bonding correlations: C H⋯O and C H⋯π. The existence of preferential orientations of the first shell coordinating molecules and the specific nature of the interactions involving the π cloud and the polar methoxy group have been reported and discussed.
Molecular dynamics of CH4/N2 mixtures on a flexible graphene layer: adsorption and selectivity case study
2019
We theoretically investigate graphene layers, proposing them as membranes of subnanometer size suitable for CH4/N2 separation and gas uptake. The observed potential energy surfaces, representing the intermolecular interactions within the CH4/N2 gaseous mixtures and between these and the graphene layers, have been formulated by adopting the so-called Improved Lennard-Jones (ILJ) potential, which is far more accurate than the traditional Lennard-Jones potential. Previously derived ILJ force fields are used to perform extensive molecular dynamics simulations on graphene's ability to separate and adsorb the CH4/N2 mixture. Furthermore, the intramolecular interactions within graphene were explic…
Microscopic structural and dynamic features in triphilic room temperature ionic liquids
2019
Here we report a thorough investigation of the microscopic and mesoscopic structural organization in a series of triphilic fluorinated room temperature ionic liquids, namely [1-alkyl, 3-methylimidazolium][(trifluoromethanesulfonyl)(nonafluorobutylsulfonyl)imide], with alkyl=ethyl, butyl, octyl ([C(n)mim][IM14], n = 2, 4, 8), based on the synergic exploitation of X-ray and Neutron Scattering and Molecular Dynamics simulations. This study reveals the strong complementarity between X-ray/neutron scattering in detecting the complex segregated morphology in these systems at mesoscopic spatial scales. The use of MD simulations delivering a very good agreement with experimental data allows us to g…
Effects of afforestation with four unmixed plant species on the soil–water interactions in a semiarid Mediterranean region (Sicily, Italy)
2012
Purpose An assessment of the effect of plant cover on the properties of four afforested soils in central Sicily was performed with the aim of discriminating among them after 60 years of afforestation. Materials and methods Chemical and biochemical soil analyses were coupled to fast field cycling (FFC) NMR relaxation investigations in order to monitor surface interactions of water in water-saturated soils. Results and discussion The traditional soil analyses revealed that the most stable soil properties such as soil texture and pH are not affected by 60 years of afforestation. Soils developed under eucalyptus trees showed larger amounts of hydrophilic organic matter as compared to the soils …
Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7
2018
AbstractNitrophorins (NP) 1–7 are NO-carrying heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus. The isoform NP7 displays peculiar properties, such as an abnormally high isoelectric point, the ability to bind negatively charged membranes, and a strong pH sensitivity of NO affinity. A unique trait of NP7 is the presence of Glu in position 27, which is occupied by Val in other NPs. Glu27 appears to be important for tuning the heme properties, but its influence on the pH-dependent NO release mechanism, which is assisted by a conformational change in the AB loop, remains unexplored. Here, in order to gain insight into the functional role of Glu27, we examine the ef…
All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome
2018
The spliceosome (SPL) is a majestic macromolecular machinery composed of five small nuclear RNAs and hundreds of proteins. SPL removes noncoding introns from precursor messenger RNAs (pre-mRNAs) and ligates coding exons, giving rise to functional mRNAs. Building on the first SPL structure solved at near–atomic-level resolution, here we elucidate the functional dynamics of the intron lariat spliceosome (ILS) complex through multi-microsecond-long molecular-dynamics simulations of ∼1,000,000 atoms models. The ILS essential dynamics unveils (i) the leading role of the Spp42 protein, which heads the gene maturation by tuning the motions of distinct SPL components, and (ii) the critical particip…