Interactions of molecular ions with model phospholipid membranes

2011 ◽  
Vol 76 (6) ◽  
pp. 695-711 ◽  
Author(s):  
Michal Petrov ◽  
Lukasz Cwiklik ◽  
Pavel Jungwirth
Keyword(s):  
Molecular Dynamics ◽  
Molecular Ions ◽  
The Other ◽  
Dynamics Simulation ◽  
Phospholipid Membrane ◽  
Biophysical Properties ◽  
Ion Specificity ◽  
Biologically Relevant ◽  
Lipid Diffusion ◽  
First Time

The affinities of a series of biologically relevant ions for a hydrated phospholipid membrane were investigated using molecular dynamics simulation. Interactions of molecular ions, such as guanidinium, tetramethylammonium, and thiocyanate with the bilayer were computationally characterized for the first time. Simulations reveal strong ion specificity. On one hand, ions like guanidinium and thiocyanate adsorb relatively strongly to the headgroup region of the membrane. On the other hand, potassium or chloride interact very weakly with the phospholipids and merely act as neutralizing counterions. Calculations also show that these ions affect differently biophysical properties of the membrane, such as lipid diffusion, headgroup hydration and tilt angle.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

2021 ◽  
Vol 22 (3) ◽  
pp. 1400
Author(s):  
Ciresthel Bello-Rios ◽  
Sarita Montaño ◽  
Olga Lilia Garibay-Cerdenares ◽  
Lilian Esmeralda Araujo-Arcos ◽  
Marco Antonio Leyva-Vázquez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Epidemiological Studies ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
Oncogenic Potential ◽  
Structural Differences ◽  
Reference Protein ◽  
E6 And E7 ◽  
First Time

The oncogenic potential of high-risk human papillomavirus (HPV) is predicated on the production of the E6 and E7 oncoproteins, which are responsible for disrupting the control of the cell cycle. Epidemiological studies have proposed that the presence of the N29S and H51N variants of the HPV16 E7 protein is significantly associated with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains uncertain. An analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose, for the first time, a 3D structure of the E7 reference protein and two of Its variants (N29S and H51N), and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

scholarly journals Variations in the Biophysical Properties of DMPG and DPPG Membranes with Staphyloxanthin: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 120 (3) ◽  
pp. 43a
Author(s):  
David R. Figueroa ◽  
John E. Cabrera ◽  
Julian Andres Melendez Delgado ◽  
Gian Pietro Miscione ◽  
Chad Leidy ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Biophysical Properties

Dynamical Behavior and Flow Mechanism of Fluid in Nanochannel by Molecular Dynamics Simulation

2009 ◽  
Author(s):  
Juanfang Liu ◽  
Chao Liu ◽  
Qin Li
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamical Behavior ◽  
Velocity Profiles ◽  
The Other ◽  
Dynamics Simulation ◽  
Nonequilibrium Molecular Dynamics ◽  
Interfacial Region ◽  
Flow Mechanism ◽  
Bulk Fluid

The flow properties and dynamical behavior of fluid in a nanochannel were investigated by nonequilibrium molecular dynamics simulation. First of all, the locale distribution of molecules in the channel is found to be strongly inhomogeneous compared to the bulk fluid. In the vicinity of the wall, portion of the fluid molecules are absorbed on the surface of wall due to the strong interaction of the atoms between the wall and liquid, so that the fluid density in the contact region would be much larger than one of the bulk fluid. But in the other region, the local density value approaches one of the bulk fluids with the increasing distance from the wall. This oscillatory behavior of density resulted in different motion behavior of molecules in the different region of nanochannel. The molecular behavior in the interfacial region is remarkably different from those of fluid atoms in the center of channel and wall atoms, which posses both the motion properties of bulk liquids and a solid atom. At the molecular level, macroscopic continuum hypothesis failed, that is, the results predicted by the Navier-Stoke equations deviate from the simulation data adopted by molecular dynamics simulation. In the paper, the velocity profiles for the channels with different width were plotted, which demonstrated that the time-averaged velocity profiles was not quadratic when the channel width was less than 10 molecular diameters. But on the other cases, the velocity profiles will agree well with the analytical solution based on the NS theory. The molecular dynamics simulation method can withdraw the important microscopical information from the simulation process, which benefit to analyze the flow mechanism at such length scale channel.

A systematic study on the intradiffusion and structure of N,N-dimethylformamide–water mixtures: by experiment and molecular dynamics simulation

RSC Advances ◽  
2016 ◽  
Vol 6 (88) ◽  
pp. 85603-85611 ◽  
Author(s):  
Jinyang Wang ◽  
Wei Gao ◽  
Haimin Zhong ◽  
Canjian Liang ◽  
Xiaojuan Chen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Systematic Study ◽  
Dynamics Simulation ◽  
Pgse Nmr ◽  
First Time

Intradiffusion coefficients ofN,N-dimethylformamide (DDMF) and water (DW) in their mixtures were measured as a function of temperature, pressure and composition for the first time using the PGSE-NMR technique.

Constant-Temperature Molecular-Dynamics Simulation of the 2D Melting Transition of Rb and K

1992 ◽  
Vol 291 ◽  
Author(s):  
J. D. Fan ◽  
Zhi-Xiong Cai
Keyword(s):  
Molecular Dynamics ◽  
Constant Temperature ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Melting Transition ◽  
Histogram Method ◽  
Graphite Intercalation ◽  
2D System ◽  
Incommensurate Structures ◽  
First Time

ABSTRACTThe energy histogram method, introduced by Ferrenberg and Swendsen [Phys. Rev. Lett., 61, 2635, (1988) and 63, 1195, (1989)], was applied for the first time to the constant temperature molecular dynamics (MD) simulation of a two-dimensional (2D) system with incommensurate structures. We performed MD simulations for the stage-2 graphite intercalation compounds (GIC's) with Rb or K being the intercalants (Rb-GIC's and K- GIC's). The temperature dependence of the specific heat, Cv, is calculated for various sizes up to 864 atoms. The melting temperature was found to be 158 K for Rb-GIC's and 119 K for K-GIC's, respectively, which are in agreement with the experimental observations.

DECOMPOSITION OF C60 MOLECULES ON Si(100)(2 × 1) SURFACE

2000 ◽  
Vol 11 (05) ◽  
pp. 1067-1076
Author(s):  
ŞAKIR ERKOÇ ◽  
ŞENAY KATIRCIOĞLU
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Phase Change ◽  
Elevated Temperatures ◽  
Model Potential ◽  
The Other ◽  
Dynamics Simulation ◽  
High Coverage ◽  
Other Hand ◽  
Low Coverage

We have investigated the decomposition of C 60 molecules with low and high coverages on Si(100)(2×1) surface at elevated temperatures. We also investigated the decomposition of an isolated C 60 molecule. We employed molecular-dynamics simulation using a model potential. It has been found that C 60 decomposes on Si(100) surface after 1000 K in the case of low coverage (0.11), however in high coverage case (0.67), C 60 molecules decompose after 900 K. On the other hand, isolated C 60 molecule decomposes after 7500 K, interestingly it shows a phase change from 3D to 2D at higher temperatures.

Short Order and Hydrogen Transport in Amorphous Palladium Materials

2009 ◽  
Vol 283-286 ◽  
pp. 149-154 ◽  
Author(s):  
E.A. Pastukhov ◽  
N.I. Sidorov ◽  
Valery A. Polukhin ◽  
V.P. Chentsov
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Molecular Dynamics Simulation ◽  
The Other ◽  
Dynamics Simulation ◽  
Hydrogen Transport ◽  
Sphere Model ◽  
Model Calculations ◽  
Function Calculation ◽  
Partial Radial Distribution Function

Molecular dynamics simulation was used for investigating hydrogen migration in Pd-Si alloy at a temperature Т = 300 K. The strong affect of hydrogen dynamics and its defects creation to structure of palladium matrix is stated. The partial radial distribution function calculation for silicon specifies a preferable arrangement of silicon atoms relative to each other in the second coordination sphere. Model calculations have shown that not only silicon atoms can affect hydrogen mobility. Hydrogen itself also can significantly change the diffusion of the other components in the alloy.

PHOTOACOUSTIC MEASUREMENT AND MOLECULAR DYNAMICS SIMULATION FOR THERMAL CONDUCTIVITY OF Al0.3Ga0.7As

2003 ◽  
Vol 14 (01) ◽  
pp. 61-72 ◽  
Author(s):  
S. CHITRA ◽  
A. JALAL ◽  
K. RAMACHANDRAN ◽  
S. RAJAGOPAL
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Thermal Property ◽  
Dynamics Simulation ◽  
Experimental Setup ◽  
Photoacoustic Technique ◽  
Photoacoustic Measurement ◽  
First Time

The thermal conductivity of Al 0.3 Ga 0.7 As is studied using photoacoustic technique and molecular dynamics simulation. Tersoff's potential is used for the simulation, for the first time, to this alloy. Thermal conductivity, determined experimentally by photoacoustic technique using our experimental setup, agrees well with the molecular dynamics simulation and literature values. The results are compared with the host GaAs and the role of DX centers in thermal property is discussed.

scholarly journals Molecular Docking and Molecular Dynamics Studies of SARS-CoV-2 Inhibitors: Crocin, Digitoxigenin, Beta-Eudesmol and Favipiravir: Comparative Study

2021 ◽  
Vol 12 (4) ◽  
pp. 5591-5600
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Comparative Study ◽  
Active Site ◽  
Antiviral Treatment ◽  
Docking Study ◽  
The Other ◽  
Dynamics Simulation ◽  
Main Protease

In this study, Crocin, Digitoxigenin, Beta-Eudesmol, and Favipiravir were docked in the active site of SARS-CoV-2 main protease (PDB code: 6LU7). The docking study was followed by Molecular Dynamics simulation. The result indicates that Crocin and Digitoxigenin are the structures with the best affinity in the studied enzyme's binding site. Still, Molecular Dynamics simulation showed that Digitoxigenin is the molecule that fits better in the active site of the main protease. Therefore, this molecule could have a more potent antiviral treatment of COVID-19 than the other three studied compounds.

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