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Former Master student in Computational physics, University of Oslo. Worked on a project in multiscale physics, where I studied the transition from quantum mechanics calculations to molecular dynamics simulations. Currently I'm a PhD student in Neuroscience. My project is part of the interdisciplinary Center for Integrative Neuroplasticity (CINPLA).
I have lately been working on a poster about brain tissue modeling and for that I have used Blender to create some graphics of neurons. In this tutorial I will show how to create a 3D model of a neuron in Blender.
Read the full tutorial here.
Professor Anders-Malthe Sørenssen was awarded the annual Olav Thon Foundation price for outstanding education. The price was awarded for his work on modernizing the physics education at the University of Oslo. He has increased the use of computational methods and challenged undergraduate students with current research problems.
Read the announcment from the Olav Thon Foundation . More information from the Department of Physics and the dean’s blog .
The classical molecular dynamics is primarily based on classical motion of atoms interacting with a given potential. Quantum molecular dynamics, on the other hand, focuses on all the interactions between atoms and electrons, and does not involve fitting interactions to experimental data. An approach to include the electronic structure is to solve the electronic Schrödinger equation, given the set of fixed nuclear positions, in each molecular dynamics step and let the nuclei to move according to classical mechanics in an effective potential due to the electrons.
In the last two weeks I have been working on calculating this effective potential, based on the results from my Hartree-Fock code. The forces acting on the nuclei are found by taking the gradient of the energy with respect to the nuclei positions. Below I have included molecular dynamics simulation of $H_2$ and $H_2O$ molecule, where the effective potential is calculated in each time step.
As a part of my master project, I have lately been working on developing a Hartree-Fock (HF) code for atomic and molecular systems. The Hartree-Fock method is the simplest many-body theory and a central starting point for most methods that describe the many-electron system more accurately. One of the advantages of HF is its low computational cost compare to more sophisticated techniques, which makes it attractive for quantum molecular dynamics studies.
Our HF code is based on gaussian basis sets, which makes the integral evaluations much easier and gives a huge computational saving. However, by taking into account the symmetries in one-body and two-body integrals, the computational cost can be reduced even further. Since the basis functions and matrix elements are real, we have the following symmetries
$$\langle i |\hat{h}|j \rangle = \langle j |\hat{h}|i \rangle $$
and
$$\langle i k|jl \rangle = \langle jk |il \rangle = \langle il |jk \rangle = \langle jl |ik \rangle =\langle ki |lj \rangle = \langle li |kj \rangle = \langle kj| li \rangle= \langle lj |ki \rangle $$
for one-body and two-body matrix elements, respectively. Having implemented these symmetries, the computation time for the ground state energy for a single water molecule (using 4-31G basis set) went from 6 sec to 1 sec, which is a huge speed up! For more details please check out this site .
Education Prize to Computational Physics!
Creating a 3D Neuron Scene in Blender
National education price awarded to Computational Physics professor
Choosing the right license for your code
Getting MCALab up and running on a 64-bit installation of Matlab on Ubuntu
Find Usages Keybind broken in QtCreator
PyCharm Keymap for QtCreator Fanatics
Fixing GDB issues with GCC 4.8.x and C++11
LaTeX package for UiO Master’s theses
Circumventing annoying library path issues with QtCreator
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