Density Functional Theory calculation on many-cores hybrid CPU-GPU architectures

The implementation of a full electronic structure calculation code on a hybrid parallel architecture with Graphic Processing Units (GPU) is presented. The code which is on the basis of our implementation is a GNU-GPL code based on Daubechies wavelets. It shows very good performances, systematic convergence properties and an excellent efficiency on parallel computers. Our GPU-based acceleration fully preserves all these properties. In particular, the code is able to run on many cores which may or may not have a GPU associated. It is thus able to run on parallel and massive parallel hybrid environment, also with a non-homogeneous ratio CPU/GPU. With double precision calculations, we may achieve considerable speedup, between a factor of 20 for some operations and a factor of 6 for the whole DFT code.Comment: 14 pages, 8 figure

Lysine Dendrimers and Their Complexes with Therapeutic and Amyloid Peptides: Computer Simulation

Lysine dendrimers consist of natural lysine amino acid residues. Due to this reason, they are usually not as toxic as other dendrimers. Lysine dendrimers are often used in drug and gene delivery. These dendrimers penetrate blood-brain barrier and thus could be used for the delivery of drugs and other substances, for example, bioactive peptides to brain or elimination of disease-related peptides out of the brain. To do it, dendrimers should form complex with these peptides. In the present chapter, we describe computer simulation of the interaction of lysine dendrimer of the second generation with three different peptides and check does it form complexes with them. Two of these peptides (Semax and Epithalon) are nootropic peptides and third is the fragment of amyloid peptide, which forms amyloid fibrils and plaques in Alzheimer’s disease. Our simulation demonstrates that the lysine dendrimers form complexes with these therapeutics peptides. Thus, we demonstrated that lysine dendrimer is a good candidate for the delivery of therapeutic peptides. We also have shown that lysine dendrimer destroys existing stacks of amyloid peptides and forms a stable complex with them. Thus, it looks that it could be used in future for the treatment of Alzheimer’s diseases

Molecular Dynamics Simulation of Dextran Extension by Constant Force in Single Molecule AFM

AbstractThe extension of 1–6 polysaccharides has been studied in a series of recent single molecule AFM experiments. For dextran, a key finding was the existence of a plateau in the force-extension curve at forces between 700 and 1000pN. We studied the extension of the dextran 10-mer under constant force using atomistic simulation with various force fields. All the force fields reproduce the experimental plateau on the force-extension curve. With AMBER94 and AMBER-GLYCAM04 force fields the plateau can be explained by a transition of the glucopyranose rings in the dextran monomers from the chair (4C1) to the inverted chair (1C4) conformation while other processes occur at smaller (rotation around C5-C6 bond) or higher (chairs to boat transitions) forces. The CHARMM force field provides a different picture which associates the occurrence of the plateau to chair-boat transitions of the glucopyranose rings

Particle-Particle, Particle-Scaling function (P3S) algorithm for electrostatic problems in free boundary conditions

An algorithm for fast calculation of the Coulombic forces and energies of point particles with free boundary conditions is proposed. Its calculation time scales as N log N for N particles. This novel method has lower crossover point with the full O(N^2) direct summation than the Fast Multipole Method. The forces obtained by our algorithm are analytical derivatives of the energy which guarantees energy conservation during a molecular dynamics simulation. Our algorithm is very simple. An MPI parallelised version of the code can be downloaded under the GNU General Public License from the website of our group.Comment: 19 pages, 11 figures, submitted to: Journal of Chemical Physic

Electroresponsive Polyelectrolyte Brushes Studied by Self-Consistent Field Theory

End-grafting of polyelectrolyte chains to conducting substrates offers an opportunity to fabricate electro-responsive surfaces capable of changing their physical/chemical properties (adhesion, wettability) in response to applied electrical voltage. We use a self-consistent field numerical approach to compare the equilibrium properties of tethered strong and weak (pH-sensitive) polyelectrolytes to applied electrical field in both salt-free and salt-containing solutions. We demonstrate that both strong and weak polyelectrolyte brushes exhibit segregation of polyions in two populations if the surface is oppositely charged with respect to the brush. This segregation gives rise to complex patterns in the dependence of the brush thickness on salt concentration. We demonstrate that adjustable ionization of weak polyelectrolytes weakens their conformational response in terms of the dependence of brush thickness on the amplitude of the applied voltage

Daubechies wavelets as a basis set for density functional pseudopotential calculations

Daubechies wavelets are a powerful systematic basis set for electronic structure calculations because they are orthogonal and localized both in real and Fourier space. We describe in detail how this basis set can be used to obtain a highly efficient and accurate method for density functional electronic structure calculations. An implementation of this method is available in the ABINIT free software package. This code shows high systematic convergence properties, very good performances and an excellent efficiency for parallel calculations.Comment: 15 pages, 11 figure

Pauli equation and the method of supersymmetric factorization

We consider different variants of factorization of a 2x2 matrix Schroedinger/Pauli operator in two spatial dimensions. They allow to relate its spectrum to the sum of spectra of two scalar Schroedinger operators, in a manner similar to one-dimensional Darboux transformations. We consider both the case when such factorization is reduced to the ordinary 2-dimensional SUSY QM quasifactorization and a more general case which involves covariant derivatives. The admissible classes of electromagnetic fields are described and some illustrative examples are given.Comment: 18 pages, Late