Methods Archives - ITN SNAL - Marie Curie Initial Training Network

Coarse-grained Molecular Dynamics

Chanfei Su — Fri, 05 Dec 2014 15:00:26 +0000

Coarse grained models are becoming increasingly popular to study systems of lipids and surfactants, which means reducing the number of degrees of freedom. Thus, in any coarse grained model there is a trade-off between accuracy in the description of the system and the gain in simulation time and length scales. Coarse grained models can be either on-lattice or off-lattice. The off-lattice model allows to include some properties more easily such as spherical particles or hydrodynamics. Smit et al1,2 have proposed a off-lattice model for an oil-water-surfactant system, in which micelles made of amphiphilic molecules form spontaneously in the water phase

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Fluoresce-Activated Cell Sorting (FACS)

Alex Chen — Wed, 05 Nov 2014 16:13:19 +0000

Flow cytometry is a laser-based biophysical technology employed in cell counting, cell sorting, and biomarker detection. Cells or materials are suspended in a stream of fluid and passed through the electronic detection apparatus. The equipment allows simultaneous multiparametric analysis of physical and chemical characteristics up to thousands of particles per second. Fluorescence-activated cell sorting (FACS) is a specialised type of flow cytometry. It provides methods for sorting a heterogeneous mixture of biological cells into two or more containers, one cell at a time, based upon the specific light scattering and fluorescent characteristics. These includes size, fluorescently labelled DNA sequence, and

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Gel permeation chromatography/ Size exclusion chromatography

Shiqi Wang — Wed, 05 Nov 2014 14:02:51 +0000

Gel permeation chromatography (GPC)/ Size exclusion chromatography (SEC) is a widely used technique for measuring the molecular weight and molecular weight distribution of natural and synthetic polymers. It is based on liquid chromatographic techniques that separate individual polymer chains on the basis of their size in solution and not on their chemical properties. The separation mechanism is shown in Figure 1: Diluted polymer solution passes through GPC column which is filled with porous beads. During the elution process, molecules with small hydrodynamic volume could enter into the pores of beads, thus taking relatively long time to pass through the column.

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Laser Scanning Confocal Microscopy (LSCM)

Mattia Morandi — Wed, 29 Oct 2014 12:51:11 +0000

Laser Scanning Confocal Microscopy (LSCM) is a fluorescence microscopy technique widely used in the biological and medical field for imaging thin optical sections in living and fixed specimens . Particularly in biophysics and biology it has become an essential tool not only to visualize lipid model membranes, but also to perform spectral imaging and diffusion rate of fluorescent probes using fluorescence recovery after bleaching (FRAP). The key principle behind confocal approach is to spatially filter the out-of focus light in specimens whose thickness exceeds the plane of focus to improve contrast and definition by discarding the background fluorescent emission from

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Neutron reflection (NR) and Small angle neutron scattering (SANS)

Daniela Ciumac — Tue, 28 Oct 2014 21:49:45 +0000

Neutron Reflection (NR) is a highly credible, non-destructive technique used to study the interfaces. It helps to define the interface properties between different material layers, and these layers can be studied with the resolution of the order of angstroms. By measuring the position of interfaces between different materials, the thickness of the layer can be obtained while the density and the contained molecular species of the studied layer can be figured out from the neutron scattering length density distribution profile . NR offers greater structural resolution, particularly with the help of deuterium labeling to lipid, solvent and lead polymeric nano-object.

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Nuclear magnetic resonance spectroscopy (NMR spectroscopy)

Shiqi Wang — Tue, 28 Oct 2014 18:17:22 +0000

Nuclear magnetic resonance spectroscopy (NMR spectroscopy) is one of the most widely used techniques by chemists and biologists to identify molecular structures. It relies on the phenomenon of nuclear magnetic resonance, which means the intramolecular magnetic around an atom in a specific molecular changes the resonance frequency. Thus, different atoms within one molecule could have different resonance signals and could be detected by the equipment. For NMR study, samples should first dissolve in deuterated solvent and prepared in a thin-wall glass tube (NMR tube). Then the NMR tubes should be installed with a spinner and put into the NMR spectrometer. Typical high resolution NMR spectrometers are

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IC – Membrane Biophysics group facilities

Anna Sofia Tascini — Tue, 28 Oct 2014 03:16:09 +0000

The Membrane Biophysics group of Imperial College of London has a range of equipment, much of which is under constant development to ensure we remain at the forefront of membrane biophysics research. They also have two fully equiped preparation labs. Please see the sections below for a more detailed description of our facilities.

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Atomistic Simulation

Anna Sofia Tascini — Tue, 28 Oct 2014 02:15:09 +0000

Atomistic simulation is the theoretical and computational modelling of what happens at the atomic scale in solids, liquids, molecules and plasmas. It could be perform throughout Molecular Statics and Molecular Dynamics . Molecular dynamics simulations follow the same approach of a real experiment: The first step is the preparation and the description of a sample of the material we wish to study. This sample is a model configuration consisting in atoms. Each elementary particle is modelled by point masses, with three degrees of freedom (,, space directions). A mass , a position , a velocity and an acceleration are associated to

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Spectroscopic ellipsometry (SE)

Daniela Ciumac — Mon, 27 Oct 2014 23:59:20 +0000

Ellipsometry is an optical technique for analyzing and characterizing an interface or a layer between two surfaces. The method is based on the measure of the change of polarization as light interacts with the material structure of interest . Ellipsometry is a very used technique, with applications in various fields, as semiconductor physics, microelectronics, biology, biophysics, telecommunications, from basic research to industrial applications . In biophysics, this method can be used to study interfacial films at solid-water interface, the structure and dynamics of interfacial adsorption of proteins, the interfacial assembly of lipids, and the interactions between various nano-objects and lipid

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Dual polarization interferometry (DPI)

Daniela Ciumac — Mon, 27 Oct 2014 23:43:48 +0000

Dual polarization interferometry is a relatively new technique, which explores the molecular layers adsorbed to the surface of a waveguide by means of an electromagnetic evanescent wave of a laser beam; it measures the refractive index and the thickness of very thin films, and is also used to study the protein adsorption at solid/water interface. Furthermore, if the refractive index of the studied film is fixed, the birefringence can be observed quantitatively so that the anisotropy of the film can be analyzed. DPI is a quantitative and real-time technique with the dimensional resolution of the order of angstroms .

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