Soft Matter & Molecular Biophysics Group    

SUGAR-PIE: Scripted Utility to Get Atomic Resolution by Positional Interpolation/Extrapolation

FOR THE IMPATIENTS (it is really easy): Click HERE to start the current version of SUGAR-PIE!

SUGAR-PIE is an application developed and maintained by Ángel Piñeiro, designed for the easy mapping of lipid bilayers from coarse-grain (CG) to atomistic (AT) resolution based on an interpolation/extrapolation approach of atomic positions. The current version works with lipid bilayers based on POPC and/or DPPC. At the moment only the MARTINI force field is available for coarse-grain level. For atomic resolution several parameterizations of the GROMOS force field, the Berger parameterization of lipids, and the CHARMM36 force field are available. The list of considered force fields and molecules is expected to increase. Note that it is possible to introduce a mixture of both lipids and even a protein embedded or interacting with the bilayer. If a protein is included in the system you should also upload an atomistic PDB file for it. The mapping back method from CG to AT resolution is quick and simple but the current version does not map molecules other than POPC and DPPC. The general description of the method can be found in this reference: DOI: 10.1039/C2SM25877C. Any type of support for this project will be highly appreciated.

For any comment, please, contact: Angel.Pineiro at usc.es

SANGRA: Script Automated Neutron Grazing Reflectivity Analysis package

FOR THE IMPATIENTS (it is really easy): Click HERE to start the current version of SANGRA!

SANGRA is a program package developed and maintained by Ángel Piñeiro, designed for the efficient massive analysis of Neutron Reflectivity profiles. Thus, SANGRA is aimed to the determination of film structures at liquid/air interfaces. The full version of SANGRA consists of a fitting engine (a Linux binary file) and several bash scripts. The fitting engine is based on the implementation of the Parrat algorithm for an arbitrary number of layers and contrasts, considering uncertainties in both the q and R values and contraints in any of the fitting parameters (thickness, roughness, scattering lenght densities, background and scaling factor). The fitting engine is also based on the numerical Simulated Annealing minimization algorithm and so the results do not depend strongly on the initial value (seed). This allows to fit a massive amount of reflectivity profiles just typing the name of a Linux script on the command line. The full version will be adapted to be used on this web site soon. A restricted version is currently available to model experimental NR profiles. For the future we aim to extend this application to produce simultaneous or independent fitting of X-ray and neutron reflectivity profiles. Any type of support for this project will be highly appreciated.

For any comment, please, contact: Angel.Pineiro at usc.es

PS: Accidentally but still worth mentioning ;) the translation of the word SANGRA from Spanish to English is BLEED

suITCase: Scripted Utility for Isothermal Titration Calorimetry Analysis & Stoichiometric Examination

FOR THE IMPATIENTS (it is really easy): Click HERE to start the current version of suITCase!

suITCase is a program package developed and maintained by Ángel Piñeiro, designed for the design/optimization and analysis of Isothermal Titration Calorimetric (ITC) experiments. The purpose of suITCase is threefold: (i) to guide in the design of ITC experiments, helping to suggest values for the parameters of the technique that can be modified by the user; (ii) to aid in the interpretation of the ITC results by providing the distribution of each chemical species as a function of the concentration ratio between both solutes; and (iii) my actual reason to develop this application is that I am trying to design materials based on one specific chemical species and this tool allows me to find the absolute concentration range under which my favorite supramolecular complex dominates the solution.

suITCase was designed to produce results for the MicroCal VP-ITC family of calorimeters. It includes the concentration and heat corrections due to the displacement of volume from the sample cell after each titration. The model implemented in the current version of suITCase is a "Sequential Binding Sites" model that considers the free species of both solutes A and B, plus the hybrid complexes with stoichimetries (1:1, 1:2, 2:1, 2:2). Of course, any subset of this model such as that involving only (1:1, 1:2) complexes or only the complexes with stoichiometry (1:1), is also included here. The general equations describing the model can be found in J. Phys. Chem. B, 2011, 115 (49), pp 14381-14396. The publicly available version of suITCase does not fit data to the model required by the user. If you require a more complex model or the fitting of experimental data instead of the single modelling of data, please do not hesitate to contact me: Angel.Pineiro at usc.es. Any type of support to maintain, speed-up or/and extend this project will be highly appreciated.

For any comment, please, contact: Angel.Pineiro at usc.es

More tools will be added to this page soon...