scholarly journals Adsorption of Silicon-Containing Dendrimers: Effects of Chemical Composition, Structure, and Generation Number

Polymers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 552
Author(s):  
Andrey O. Kurbatov ◽  
Nikolay K. Balabaev ◽  
Mikhail A. Mazo ◽  
Elena Yu. Kramarenko
Keyword(s):  
Molecular Dynamics ◽  
Functional Materials ◽  
Md Simulations ◽  
Conformational Behavior ◽  
Carbosilane Dendrimers ◽  
Density Profiles ◽  
The Core ◽  
Adsorbed Atoms ◽  
Composition Structure ◽  
Surface Spreading

We studied the conformational behavior of silicon-containing dendrimers during their adsorption onto a flat impenetrable surface by molecular dynamics (MD) simulations. Four homologous series of dendrimers from the 4th up to the 7th generations were modeled, namely, two types of carbosilane dendrimers differing by the functionality of the core Si atom and two types of siloxane dendrimers with different lengths of the spacers. Comparative analysis of the fractions of adsorbed atoms belonging to various structural layers within dendrimers as well as density profiles allowed us to elucidate not only some general trends but also the effects determined by dendrimer specificity. In particular, it was found that in contrast to the carbosilane dendrimers interacting with the adsorbing surface mainly by their peripheral layers, the siloxane dendrimers with the longer –O–Si(CH3)2–O spacers expose atoms from their interior to the surface spreading out on it. These findings are important for the design of functional materials on the basis of silicon-containing dendrimers.

scholarly journals Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments

Membranes ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 507
Author(s):  
Nebojša Zec ◽  
Gaetano Mangiapia ◽  
Alex C. Hendry ◽  
Robert Barker ◽  
Alexandros Koutsioubas ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Scattering Length ◽  
Md Simulations ◽  
Real Space ◽  
Scattering Data ◽  
Phospholipid Membrane ◽  
Density Profiles ◽  
X Ray ◽  
Angle Scattering ◽  
Scattering Measurements

We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually possible to retrieve this profile unambiguously from the data alone. MD simulations predict these density profiles, but they require experimental control. Both issues can be addressed simultaneously by cross-validating scattering data and MD results. The strengths and weaknesses of each technique are discussed in detail with the aim of optimizing the opportunities provided by this combination.

scholarly journals Structural and dynamical anomalies of soft particles interacting through harmonic repulsions

2015 ◽  
Vol 17 (8) ◽  
pp. 5734-5742 ◽  
Author(s):  
Wenze Ouyang ◽  
Bin Sun ◽  
Zhiwei Sun ◽  
Shenghua Xu
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
The Core ◽  
Soft Particles

Molecular dynamics (MD) simulations are carried out to investigate the structural and dynamical anomalies in the core-softened fluid with harmonic repulsions.

scholarly journals Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

2019 ◽  
Vol 3 (4) ◽  
pp. 24
Author(s):  
Marie-Anne Hervé du Penhoat ◽  
Anis Hamila ◽  
Marie-Pierre Gaigeot ◽  
Rodolphe Vuilleumier ◽  
Kentaro Fujii ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
X Rays ◽  
Auger Decay ◽  
Hydration Layer ◽  
The Core ◽  
Dynamics Simulations

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

scholarly journals Functional and Structural Analysis of Predicted Proteins Obtained from Homo sapiens’ Minisatellite 33.15-Tagged Transcript pAKT-45 Variants

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Mohd Shahbaaz ◽  
Awad Saeed Al-Samghan ◽  
Arshi Malik ◽  
Sarah Afaq ◽  
Afaf S. Alwabli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Homo Sapiens ◽  
Md Simulations ◽  
Early Embryogenesis ◽  
Cellular Proteins ◽  
Conformational Behavior ◽  
Gene Functions ◽  
Mrna Transcripts ◽  
Water Conditions ◽  
Explicit Water

The spermatozoa are transcriptionally dormant entities which have been recognized to be an archive of mRNA, coding for a variety of functionally crucial cellular proteins. This significant repository of mRNA is predicted to be associated with early embryogenesis and postfertilization. The mRNA transcripts which are tagged with minisatellites have been involved in the regulation of the gene functions as well as their organization. However, very little information is available regarding the expression of the transcripts tagged with minisatellites in spermatozoa. Therefore, in order to understand the functions and the conformational behavior of the proteins expressed from these minisatellite-tagged transcripts, we have performed a detailed in silico analysis using the sequences of the transcripts. The protein predicted from KF274549 showed the functionalities similar to uncharacterized C4orf26 proteins, while that obtained from KF274557 predicted to be a metallophosphoesterase. Furthermore, the structural folds in the structure of these predicted proteins were analyzed by using the homology modeling and their conformational behaviors in the explicit water conditions were analyzed by using the techniques of Molecular Dynamics (MD) simulations. This detailed analysis will facilitate the understanding of these proteins in the spermatozoon region and can be used for uncovering other attributes of the metabolic network.

The Surface Tension of Nanobubbles and the Effect of the Potential Cutoff Radius

2010 ◽  
Author(s):  
Ian A. Cosden ◽  
Jennifer R. Lukes
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Strong Dependence ◽  
Md Simulations ◽  
Density Profiles ◽  
Curvature Effects ◽  
Lennard Jones ◽  
Transverse Pressure ◽  
Cutoff Radius ◽  
Interaction Cutoff

Molecular dynamics (MD) simulations are carried out to calculate the surface tension of bubbles formed in a metastable Lennard-Jones (LJ) fluid. The calculated normal and transverse pressure components are used to compute a surface tension which is compared to the surface tension computed from the Young-Laplace equation. Curvature effects on surface tension are investigated by performing various sized simulations ranging from 6,912 to 256,000 LJ particles. Density profiles, pressures, and calculated surface tension are shown to have a strong dependence on the choice of the interaction cutoff radius. A cutoff radius of 8σ, significantly larger than that commonly used in the literature, is recommended for accurate calculations in liquid-vapor systems.

Effect of Particle Shape on Neck Growth and Shrinkage of Nanoparticles

2017 ◽  
Author(s):  
Elham Mirkoohi ◽  
Rajiv Malhotra
Keyword(s):  
Thin Film ◽  
Molecular Dynamics ◽  
Flexible Electronics ◽  
Particle Shape ◽  
Functional Materials ◽  
Md Simulations ◽  
Neck Growth ◽  
Nanoparticle Shape ◽  
Temperature Ramps ◽  
Thin Film Devices

Sintering of nanoparticles to create films and patterns of functional materials is emerging as a key manufacturing process in applications like flexible electronics, solar cells and thin-film devices. Further, there is the emerging potential to use nanoparticle sintering to perform additive manufacturing as well. While the effect of nanoparticle size on sintering has been well studied, very little attention has been paid to the effect of nanoparticle shape on the evolution of sintering. This paper uses Molecular dynamics (MD) simulations to determine the influence of particle shape on shrinkage and neck growth for two common nanoparticle shape combinations, i.e., sphere-sphere and sphere-cylinder nanoparticles of different sizes. These sintering indicators are examined at two different temperature ramps. The results from this work show that depending on their relative sizes, degree of neck growth and shrinkage are both significantly affected by the nanoparticle shape. The possibility of using this phenomenon to control density and stresses during nanoparticle sintering are discussed.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

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