DPPCPhospholipid MembranesLipidsBilayerCell membraneLipid BilayersPhysicochemical propertiesMonolayersPermeabilityPeptidesGlycolipidsProteinUltrasoundBacterialInterfacesLemkulStructuralComputationalCholesterolFundamentalDimersBiological processesMoleculesPhysicsBehaviorProteinsCalculationsLevelChemistryTutorialJournalStudiesAnalysisSoftwareDrugShownResults
DPPC9
- Experiments on bilayers and monolayers containing lipids such as dipalmitoylphosphatidylcholine (DPPC) provide the essential target data for this project. (nih.gov)
- Dipalmitoylphosphatidylcholine (DPPC) is a phospholipid (and a lecithin) consisting of two C16 palmitic acid groups attached to a phosphatidylcholine head-group. (wikipedia.org)
- Among the phospholipids, the most prevalent one is phosphatidylcholine (PC, or lecithin) (70-85%), which in turn is the basis of a pool of similar diacylphophatidylcholines of which 50% is dipalmitoylphosphatidylcholine or DPPC. (wikipedia.org)
- More specifically, it has been found that phosphatidylcholine (PC) is the most abundant phospholipid (70%-85%), and that PC is primarily present as dipalmitoylphosphatidylcholine (DPPC). (wikipedia.org)
- We have modelled a flat bilayer and a liposome composed of dipalmitoylphosphatidylcholine (DPPC), using molecular dynamics simulation. (bvsalud.org)
- This work investigates how docosahexaenoic acid (DHA) modifies the effect of Cholesterol (Chol) on the structural and dynamical properties of dipalmitoylphosphatidylcholine (DPPC) membrane. (nutrition-evidence.com)
- In this work, the formation of aqueous lipid/nanoparticle assemblies (LNAs) consisting of hydrophobic silver-decanethiol particles (5.7 ± 1.8 nm) embedded within 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers is demonstrated as a function of the DPPC/Ag nanoparticle (AgNP) ratio. (biomedcentral.com)
- Visualization of a similar molecular dynamics simulation using DPPC membranes with an embedded protein. (rescale.com)
- A phospholipid membrane, consisting of 1024 dipalmitoylphosphatidylcholine (DPPC) lipids in a bilayer configuration with 23 water molecules per lipid, for a total of 121,856 atoms. (rescale.com)
Phospholipid Membranes3
- 2] Alsop, R. J., Maria, Schober R., and Rheinstadter, M. C. Swelling of Phospholipid Membranes by Divalent Metal Ions Depends on the Location of the Ions in the Bilayers. (sciendo.com)
- For kinetic transport of biochemical compounds or drug molecules, the permeability through the phospholipid membranes is a key kinetic property, but long timescales are hindering the accurate computation. (bvsalud.org)
- EPA and DHA replace arachidonic acid (ARA) in the phospholipid membranes. (nutrition-evidence.com)
Lipids6
- To this end a combination of high level quantum mechanical calculations and molecular dynamics (MD) simulation are carried out on model compounds, compared with experiment, and then applied to lipids and related compounds. (nih.gov)
- During the last decades, the approach to overcome the complexity of biological membranes is to use simplified biomimetic models mainly consisting of binary or ternary mixtures of lipids [ 1 , 2 ]. (hindawi.com)
- One of the most debated issues in the biophysics of lipids is lipid miscibility and its relevance to the function and organization of biological membranes. (hindawi.com)
- MARV assembles and buds from the host cell plasma where MARV matrix protein (mVP40) dimers associate with anionic lipids at the plasma membrane inner leaflet and undergo a dynamic and extensive self-oligomerization into the structural matrix layer. (uci.edu)
- An advantage of using lipids as stabilizing or functional ligands is that they mimic the lipidic scaffolding of biological membranes and have well-characterized physicochemical properties and phase behavior. (biomedcentral.com)
- Likewise, Jang et al [ 7 ] embedded 2.5-3.5 nm silicon particles with chemisorbed 1-octanol into bilayer membranes composed of DOXYL-labeled phosphocholine lipids. (biomedcentral.com)
Bilayer2
- Impact of A2T and D23N Mutations on Tetrameric Aβ42 Barrel within a Dipalmitoylphosphatidylcholine Lipid Bilayer Membrane by Replica Exchange Molecular Dynamics. (ibpc.fr)
- Bilayer systems are frequently studied as models of biological membranes. (lookformedical.com)
Cell membrane3
- The broad research goal of these projects is to simulate a cell membrane on the atomic level. (nih.gov)
- These peptides are excreted from amphibian skin, and can interact with and disrupt bacterial membranes, leading to the permeabilisation of the cell membrane. (bicnirrh.res.in)
- In spite of the relevance of lipid-protein interactions, the phase behaviour of the lipid components of the cell membrane is believed to be of major importance to uncover some underlying principles behind the membrane function. (hindawi.com)
Lipid Bilayers1
- Synthetic phospholipid used in liposomes and lipid bilayers to study biological membranes. (lookformedical.com)
Physicochemical properties1
- At the micro-scale (atomic level), we use tools from molecular modeling and molecular simulations to understand the physicochemical properties that govern intercellular communication mediated by gap-junction channels, the structure and function of water at the nanoscale, and molecular recognition and signal transduction processes mediated by proteins. (cienciavida.org)
Monolayers1
- Ionic environment, thickness and line tension as determinants of phase separation in whole Purified Myelin Membranes monolayers. (tu-darmstadt.de)
Permeability1
- It is first reviewed how RETIS, a path-sampling methodology that gives in principle exact kinetics, can be used to compute membrane permeability. (bvsalud.org)
Peptides4
- The Curvature Induction of Surface-Bound Antimicrobial Peptides Piscidin 1 and Piscidin 3 Varies with Lipid Chain Length," B. S. Perrin Jr., A. J. Sodt, M. L. Cotten and R. W. Pastor, Journal Of Membrane Biology , 248 (3, SI) pp. 455-467 (2015). (nih.gov)
- The caerin 1 peptides are among the most powerful of the broad-spectrum antibiotic amphibian peptides [PMID: 12717721]. (bicnirrh.res.in)
- We conducted molecular dynamics simulations of Asp and Glu peptides in the presence of calcium and chloride ions to elucidate the underlying phenomena. (uni-konstanz.de)
- In line with experimental differences, in our simulations, we indeed find strong differences in the way the peptides interact with ions in solution. (uni-konstanz.de)
Glycolipids2
- The current principal focus of this project is the development of molecular mechanic force fields (FF) suitable for atomic level simulations of simple and complex bilayers, including glycolipids. (nih.gov)
- Interplay of trans- and cis-interactions of glycolipids in membrane adhesion. (tu-darmstadt.de)
Protein2
- This feature-based graph embedding of temporal protein graphs makes it possible to apply the general descriptive power of RIN formalisms to the analysis of protein simulations of complex processes such as protein folding and multidomain interactions requiring no protein-specific input. (uni-konstanz.de)
- We demonstrate this on simulations of the fast folding protein Trp-Cage and the multidomain signaling protein FAT10. (uni-konstanz.de)
Ultrasound2
- We employ low-cost and non-invasive methods: zeta potential (ZP), conductivity, density, and ultrasound velocity, complemented by molecular dynamics simulations. (nutrition-evidence.com)
- 2019. Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level . (ibpc.fr)
Bacterial2
- They seem to exert a lytic action on bacterial membranes. (bicnirrh.res.in)
- Lipopolysaccharides at Solid and Liquid Interfaces: Models for Biophysical Studies of the Gram-negative Bacterial Outer Membrane. (tu-darmstadt.de)
Interfaces2
- Ionic Surfactants at Air/Water and Oil/Water Interfaces: A Comparison Based on Molecular Dynamics Simulations. (tu-darmstadt.de)
- We have simulated a hexadecyltrimethylammonium (CTA) chloride monolayer adsorbed at the water/air and water/1,2-dichloroethane (DCE) interfaces. (chemistrybits.com)
Lemkul1
- 1] Allen, W. J., Lemkul, J. A., and Bevan, D. R. GridMAT-MD: a Grid-Based Membrane Analysis Tool for Use With Molecular Dynamics. (sciendo.com)
Structural1
- Here, we aim to assess how structural aspects of caveolae, the curvature of the membrane, influence the local oxygen abundance and the membrane partitioning. (bvsalud.org)
Computational2
- Assessing kinetics in biological processes with molecular dynamics simulations remains a computational and conceptual challenge, given the large time and length scales involved. (bvsalud.org)
- Gonzalez A., Duran Sepulveda L., Araya-Secchi R., Garate J. A., Pessoa-Mahana C. D., Lagos C. F. and Perez-Acle T. Computational modeling study of functional microdomains in cannabinoid receptor type 1. (cienciavida.org)
Cholesterol1
- We have hypothesized that curved and cholesterol-enriched membrane invaginations called caveolae help maintain the proper oxygen level by taking up oxygen and attenuating its release to the mitochondria. (bvsalud.org)
Fundamental1
- NMR spin lattice relaxation) are also developed both to supplement experiment and to provide further insight into the fundamental physics of membrane structure and dynamics. (nih.gov)
Dimers1
- High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields. (ibpc.fr)
Biological processes1
- Whilst our main goal is to produce a tool for multi-scale simulation of biological systems, we also study biological processes at single scales. (cienciavida.org)
Molecules2
- Molecular dynamics simulations of the liquid−vapor interface of aqueous solutions of sodium fluoride and of sodium iodide have been carried out using nonpolarizable force fields for ions and water molecules. (chemistrybits.com)
- We report a study on the effects of the amount of oil (100, 300, and 1372 1,2-dichloroethane molecules) spread on a hexadecyltrimethylammonium (CTA) chloride monolayer adsorbed on water. (chemistrybits.com)
Physics1
- To do so, we use and produce computer-based simulation tools by combining advanced mathematical modeling, thermodynamics, physics and chemistry, together with high performance computing (HPC) techniques. (cienciavida.org)
Behavior1
- We here investigate how mutations and glycosylation interfere with AGP's conformational dynamics changing its biophysical behavior, by using molecular dynamics (MD) simulations and sequence-based dynamics predictions. (bvsalud.org)
Proteins2
- This family consists of several caerin 1 proteins from Litoria species, Australian tree frogs. (bicnirrh.res.in)
- α-1 acid glycoprotein (AGP) is one of the most abundant plasma proteins. (bvsalud.org)
Calculations1
- The calculations are carried out by means of molecular dynamics simulations. (chemistrybits.com)
Level1
- Based on our simulation data, we identified three reasons contributing to these differences, leading to a new level of understanding additive-ion interactions. (uni-konstanz.de)
Chemistry5
- Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation using NMR Data," R. M. Venable, Y. Luo, K. Gawrisch, B. Roux and R. W. Pastor, Journal of Physical Chemistry B , 117 pp. 10183-10192 (2013). (nih.gov)
- Development of the simulation programs such as CHARMM (Chemistry at HARvard Molecular Mechanics) is also carried out as part of this project. (nih.gov)
- JOURNAL OF RESEARCH of the National Bureau of Standards - A.Phys ics and Chemistry 1977;81A(1):89-96. (sciendo.com)
- The Journal of Physical Chemistry B 5-2- 2015b;119(5):1947-56. (sciendo.com)
- In our scientific activity at the Division of Physical Chemistry 1 we find it essential to establish long-term goals and policies that are based on an unbiased analysis of the specific situation, rather than an uncritical following of the current trends. (lu.se)
Tutorial3
- This tutorial will introduce you to a basic molecular dynamics simulation in Gromacs on Rescale. (rescale.com)
- This tutorial will use one run of the Gromacs simulation to output the final results. (rescale.com)
- For example, Tutorial 2: Molecular Dynamics) To change the name of your project, click on the pencil (shown in blue, below) next to the current job name in the top left corner of the window. (rescale.com)
Journal1
- Journal of Membrane Biology 2010;235(1):43-50. (sciendo.com)
Studies3
- Studies have shown that infection, excessive coagulation, cytokine storm, leukopenia, lymphopenia, hypoxemia and oxidative stress have also been observed in critically ill Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) patients in addition to the onset symptoms. (nutrition-evidence.com)
- In contrast, some studies have reported that EPA and DHA can make cell membranes more susceptible to non-enzymatic oxidation mediated by reactive oxygen species, leading to the formation of potentially toxic oxidation products and increasing the oxidative stress. (nutrition-evidence.com)
- In 1997, Simons and Ikonen renewed the interest in lipid phase studies, suggesting that lateral phase separation in biological membranes could be functionally important [ 3 ]. (hindawi.com)
Analysis1
- Due to an error in an analysis program, Fig. 4A in our Letter [1] was incorrectly plotted. (chemistrybits.com)
Software2
- The resultant images are captured on conventional high resolution photographic film [1] , digitized using a standard flatbed scanner, and then subjected to computer processing using a standard PC running MS Windows to yield a 3-dimensional image which can be further manipulated, based on available software and the investigators' objectives. (chronopause.com)
- The serial images obtained using TEM are aligned and stacked, at which point software is used to render a 3-dimensional representation of the imaged tissue ( Figure 2 and Figure 19 ). (chronopause.com)
Drug1
- Hybrid lipid/nanoparticle conjugates provide a biologically inspired means of designing stable agents for biomedical imaging, drug delivery, targeted therapy, and biosensing [ 1 ]. (biomedcentral.com)
Shown2
- [8] The process of USSTEM is shown in Figure 1 . (chronopause.com)
- An illustration of a vesicle assembly is shown in Figure 1 (not to scale). (biomedcentral.com)
Results2
- Results obtained in this work shed light on the effect of polyunsaturated fatty acids - particularly DHA - on lipid membranes, with potential preventive applications in many diseases, e.g. neuronal as, Alzheimer's disease, and viral, as Covid-19. (nutrition-evidence.com)
- Alternatively, you can also click the Get Job Results link above, and review the full setup and results for the molecular dynamics simulation with Gromacs. (rescale.com)