In our previous article about construction of the discrete Laplacian with numpy we discuss the discrete Laplacian calculation for numerical solving of diffusion PDE. Here we generalize this technique for the  two-dimensional space. We describe the complete algorithm of solving of reaction-diffusion equations with implementation of Crank-Nicolson scheme for diffusion part together with Runge-Kutta scheme for […]

continue reading.....

In this article we consider calculation of discrete Laplacian for 1D arrays using python/numpy/scipy. We introduce the sparse matrix technique that is rather efficient for computation of certain types of diffusion PDE.

continue reading.....

Here is the tutorial about how to scan potential energy over specific internal coordinate (e.g. dihedral angle) ab initio and then transfer this trajectory into molecular mechanics package and compare them.

continue reading.....

FRAP kinetics can be measured from image series directly with numpy libraries. However sometimes it is necessary to remove motion of the sample before measuring fluorescence intensity. In such a case it is possible to use normalized cross-correlation technique. Here we provide script that helps you to remove sample motion and obtain FRAP kinetics from […]

continue reading.....

With QM software like GAMESS/Firefly it is possible to obtain much information about a molecule in text format. There exist some «envelope» software like Gabedit or WxMacMolPlt that could help you to visualize this information. Here we provide some instructions that will allow you to make your own visualization using powerful abilities of PyMol. Below […]

continue reading.....

The following application solves 1d Schrodinger equation in user defined potential. The app is written in Python and uses Numpy,SciPy for linear algebra and Matplotlib for visualization. The program can be used as a standalone application as well as python module implementing relevant calculations. Atomic units are used througout the interface. The precision of calculations […]

continue reading.....

This PyMol script is capable of generating a set of a molecule’s conformations, which can be further used to calculate their potential energy or any other properties. The script enables one to vary several internal degrees of freedom (DOFs) synchronously as well as scanning over a multidimensional grid in a space of DOFs. To use […]

continue reading.....

Построение лицеприятных графиков в matplotlib сопряжено с рядом технических трудностей. Для того, чтобы график был хорошо читаем приходится настраивать большое количество параметров, как то шрифт подписей, толщину линий ошибки, легенду, частоту подписей осей, шаг сетки и многое другое. В данной статье подробно разбирается построение одного графика, на примере которого Вы можете составить свой собственный скрипт.

continue reading.....

Скачать программу (правая кнопка — сохранить как) Дополнительное ПО, необходимое для корректной работы программы под Windows

continue reading.....

Программа TRAX позволяет численно решать системы обыкновенных дифференциальных уравнений и визуализировать решение в виде графиков от времени либо траекторий на фазовой плоскости. Также программа позволяет численно решать системы разностных (дискретных) уравнений. Для уcтановки программы необходимо выполнить следующие действия: Установить интерпретатор языка Python и набор вспомогательных библиотек, входящих в состав Enthought Python Distribution (EPD). Скачать EPD […]

continue reading.....