Tuesday, 1 March 2016

Palestra realizada no departamento de Fisica da Universidade Nacional Mayor de San Marcos o dia 29/02/2016 em Lima-Peru

Monday, 21 September 2015

Benzoic acid interacting with stearic acid --> Environmental applications

Mixed organic films composed of molecules with differing hydrophobic groups are relevant to environmental interfaces such as the surface of atmospheric aerosols due to the complex composition of atmospheric emissions.Aromatics are a known component of crude oil, and once released into the atmosphere through an event such as an oil
spill, they can be weathered to produce varying degrees of oxidized products like benzaldehyde or benzoic acid. Molecules released through such anthropogenic processes are shown here to have complex interactions with organics released through biogenic emissions (like stearic acid) at the aqueous interface, resulting in diverse surface morphologies that may have an effect on the aerosol particle’s overall effect on atmospheric chemistry and climate.
 In this video they are studied using MD simulations, showing modifications to the surface due to both the hydrophobic and hydrophilic identity of the aromatic molecules.  For more information http://pubs.acs.org/doi/abs/10.1021/jp402737n

Saturday, 6 November 2010

Hydrophobic hydration of heme




In this video the hydration of the heme in water is shows. The oxygens and hydrogens of the water are represented in red and gray color respectively. The surfaces represent the probability to find the atom and are related to the region of hight density. We found densities about four times the water density (at normal condition), its is consequent of the hydrophobic effect and accommodations not tetrahedral.

Monday, 10 August 2009

How to analyze the AutoDock results?


In this video we show the analysis of the output of the AutoDock program.
Showing the secondary structure of the protein, the grid used in the rigid docking calculation and the two predominant conformations of the ligand in the binding site.
This work was developed by Teobaldo Cuya (PUC-Rio, Brazil.2009)

Saturday, 8 August 2009

Molecular dynamics of the human serum albumin with two docked Protoporphyrins IX


This is an interval of the trajectory of a molecular dynamic simulation of the human serum albumin with two docked Protoporphyrins IX. This work was developed by Teobaldo Cuya (PUC-Rio, Brazil, 2009)

Second binding site of the Protoporphyrin IX in HSA


Using docking (AutoDock) and molecular dynamics (Gromacs ) in a simulation of 10 ns, we found the possible second binding site of this porphyrin. There are experimental information about the existence of this site, but their position in the protein is not determined. With this simulation we proposed this position (article in progress to be publicate). This work was developed by Teobaldo Cuya (PUC-Rio, Brazil, 2009).

Wednesday, 5 August 2009

Parametrization necessary to model a molecule


This video was made in the LMDM (Laboratorio de Modelagem e Dinamica Molecular) of the IBCCF (Instituto de Biofisica Carlos Chagas Filho da UFRJ.

Tuesday, 4 August 2009

Electrostatic Surface of the Human Serum Albumin


We obtained the electrostatic surface using the PMV program with the aproximation Poisson-Boltzman. This surface was obtained at the end of 20 ns MD with the albumin docked with two protoporphyins IX (PPIX). As we can observed the second site of the of the PPIX molecule is localized in the central region. This work was developed by Teobaldo Cuya (PUC-Rio, Brazil, 2009).

Saturday, 1 August 2009

Firts principal component of the human serum albumin in a molecular dynamics of 100 ns.


In order to make an analysis of relevant motions in the protein, we need to eliminated the no relevant motions (rotation + translation). With this filtered trajectory we make a diagonalization of the covariance matrix (matrix of the fluctuations), obtained the corresponding eigenvectors and eigenvalues. These relevant motions has biological importance in the bind and liberation of molecules.
The eigenvectors are the main motions and the corresponding eigenvalues are the amplitude of these motions. The first eigenvector has the more biggest contribution to total motion.
Here we show the first eigenvector of the human serum albumin in aqueous medium. This result was obtained from a molecular dynamics of 100 ns (using Gromacs). This work was developed by Teobaldo Cuya (PUC-Rio, Brazil, 2009).