1. Density matrix algorithms in electronic structure theory

2. Coarse-grained simulations with dissipative particle dynamics

ALexander Lyubartsev, Alexander Mirzoev

We will use the inverse Monte Carlo method to prepare coarse-grained models for simulations of soft matter at the meso scale. Using input from atomistic molecular dynamics (atom-atom distribution functions) the IMC method allows to construct effective potentials that makes it possible to coarse grain the simulations to reach much larger time and lenght scales. As an example we construct water mediated potentials which can be used to simulate ion dynamics around macromolecules (DNA, RNA) on a long time scale.

4. First principles modeling of nanoelectronics

5. Embedding quantum mechanical systems in classical environments

6. Merging electronic structure calculations with large scale simulations of spin dynamics

Jacob Kongsted, Kestutis Aidas

In this computer exercise newly developed quantum mechanics/molecular mechanics (QM/MM) methods will be used for theoretical prediction and rationalization of molecular properties of extended systems. All essential steps in the procedure will be covered, e.g. molecular dynamics simulations, preparation of the QM/MM input files, conduction of the QM/MM calculations and interpretation and rationalization of the final predictions. The focus will be on molecular spectroscopic properties such as UV and NMR parameters. (Half-week exercise followed by exercise Nr. 7b)

7b. Quantum mechanics - Wave mechanics modelling of optical properties and laser propagation

Faris Gelmukhanov, Yuping Sun

In this project we will consider a special case of multiscale modelling, sometimes called multiphysics modelling, where quantum mechanics and wave mechanics are combined. We start by computing some simple cross sections for light absorption and emission by means of quantum mechanics (respons method), we solve the so-called density matrix equation to get the overall level populations, and, using this information we solve Maxwells equations to get the macroscopic light properties of the material, and find out how the laser pulse propagates. We can make chemical modifications and see how this might change the optical properties of the material. (Half-week exercise followed by exercise Nr. 7a)

Anders Niklasson

A majority of current state-of-the-art reduced complexity schemes in electronic structure theory avoid the O(N^3) scaling of the quantum mechanical eigenvalue problem by solving for the density matrix instead of the wavefunctions. There are several important open questions still remaining and further optimizations to be made that can be studied in this computational project.

A majority of current state-of-the-art reduced complexity schemes in electronic structure theory avoid the O(N^3) scaling of the quantum mechanical eigenvalue problem by solving for the density matrix instead of the wavefunctions. There are several important open questions still remaining and further optimizations to be made that can be studied in this computational project.

2. Coarse-grained simulations with dissipative particle dynamics

Zhongyuan Lu

The exercises are intended to show the technical issues about the dissipative particle dyanmics (DPD). For those unfamiliar with DPD, some of the basic exercises will show the structure of the algorithms. Several integration schemes will be presented for a better comparison between molecular dynamics and DPD. Beyond these, some of the exercises will deal with the practical issues when DPD is used as a coarse-grained simulation tool to study, for example, the self-assembly of surfactants, the dynamic scaling of polymers, and block copolymer melts under shear. Mapping from a real system to DPD model (coarse-graining) is also concerned.

The exercises are intended to show the technical issues about the dissipative particle dyanmics (DPD). For those unfamiliar with DPD, some of the basic exercises will show the structure of the algorithms. Several integration schemes will be presented for a better comparison between molecular dynamics and DPD. Beyond these, some of the exercises will deal with the practical issues when DPD is used as a coarse-grained simulation tool to study, for example, the self-assembly of surfactants, the dynamic scaling of polymers, and block copolymer melts under shear. Mapping from a real system to DPD model (coarse-graining) is also concerned.

3. Inverse Monte Carlo mesoscale simulations

ALexander Lyubartsev, Alexander Mirzoev

We will use the inverse Monte Carlo method to prepare coarse-grained models for simulations of soft matter at the meso scale. Using input from atomistic molecular dynamics (atom-atom distribution functions) the IMC method allows to construct effective potentials that makes it possible to coarse grain the simulations to reach much larger time and lenght scales. As an example we construct water mediated potentials which can be used to simulate ion dynamics around macromolecules (DNA, RNA) on a long time scale.

4. First principles modeling of nanoelectronics

Bin Gao, and Yi Luo

Nanostructures possess a great challenge for theoretical modeling since they often consist of a huge number of electrons without periodic boundary conditions. In this project we will make us of our computational approach, named the central insertion scheme (CIS), which allows to calculate electronic structure of nanomaterials at a first principles level. With the help of parallel programming, our package BioNano-LGEO can handle systems consisting of tens of thousands of electrons with reasonable computational effort. We will learn how to use the CIS method to calculate electronic structures of conjugated polymers, carbon nanotubes and other nanostructures of your own interest. In combination with the QCME (Quantum Chemistry for Molecular Electronics) package, also developed in our group, we calculate electrnic cunductance and current-voltage characteristics of the nanostructures under investigation.

Nanostructures possess a great challenge for theoretical modeling since they often consist of a huge number of electrons without periodic boundary conditions. In this project we will make us of our computational approach, named the central insertion scheme (CIS), which allows to calculate electronic structure of nanomaterials at a first principles level. With the help of parallel programming, our package BioNano-LGEO can handle systems consisting of tens of thousands of electrons with reasonable computational effort. We will learn how to use the CIS method to calculate electronic structures of conjugated polymers, carbon nanotubes and other nanostructures of your own interest. In combination with the QCME (Quantum Chemistry for Molecular Electronics) package, also developed in our group, we calculate electrnic cunductance and current-voltage characteristics of the nanostructures under investigation.

5. Embedding quantum mechanical systems in classical environments

Tomasz Wesolowski

In this project we will numerically study some aspects of embedding techniques based on the orbital-free embedding potential. In such techniques, a small quantum mechanical system is inserted into an environment which is characterized only by its electron density and can be, therefore, of any size from microscopic to macroscopic. Model systems where the exact embedding potential is available and real systems where the potential is approximated will be analyzed. As an example, we will study complexation induced shifts on the electronic excitation energies resulting from the interaction between an organic chromophore and hydrogen bonded molecules. This will be obtained following the formalism combining the orbital-free embedding potential with time-dependent DFT for the excitation energies.

6. Merging electronic structure calculations with large scale simulations of spin dynamics

Olle Eriksson

7a. Calculation of molecular properties using hybrid quantum mechanics/molecular mechanics methodologies.Spin excitations in a material can take place on several length scales, and modeling these excitations is a typical example of multiscale modeling. The project on atomistic spin dynamics, couples information from the electronic structure and how it describes interatomic exchange parameters, with langevin dynamics on the atomistic spin system. The project involves learning the langevin dynamics part in some detail and the calculations of exchange parameters to a lesser degree. Simulations will be done on typical magnetic materials like bcc Fe and skyrmion like magnetic structures.

Jacob Kongsted, Kestutis Aidas

In this computer exercise newly developed quantum mechanics/molecular mechanics (QM/MM) methods will be used for theoretical prediction and rationalization of molecular properties of extended systems. All essential steps in the procedure will be covered, e.g. molecular dynamics simulations, preparation of the QM/MM input files, conduction of the QM/MM calculations and interpretation and rationalization of the final predictions. The focus will be on molecular spectroscopic properties such as UV and NMR parameters. (Half-week exercise followed by exercise Nr. 7b)

Faris Gelmukhanov, Yuping Sun

In this project we will consider a special case of multiscale modelling, sometimes called multiphysics modelling, where quantum mechanics and wave mechanics are combined. We start by computing some simple cross sections for light absorption and emission by means of quantum mechanics (respons method), we solve the so-called density matrix equation to get the overall level populations, and, using this information we solve Maxwells equations to get the macroscopic light properties of the material, and find out how the laser pulse propagates. We can make chemical modifications and see how this might change the optical properties of the material. (Half-week exercise followed by exercise Nr. 7a)