Slawomir Orlowski

Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin.

The physiological role of recently discovered human neuroglobin (Ngb) is still unknown. Sound hypothesis says that it protects brain during hypoxia. In this paper the advanced potential of mean force by implicit ligand sampling (PMF/ILS) method is used to study the free energy landscape of Ngb for O(2), NO and CO ligands. The multiple diffusion paths are discovered and four ligand binding cavities are determined. The data show that certain regions are easily accessible by O(2) and NO but are protected from CO. Free energy landscapes provide realistic data for stochastic models of ligand diffusion in proteins.

Parallel implementation of the DGF-FDTD method on GPU Using the CUDA technology

The discrete Greens function (DGF) formulation of the finite-difference time-domain method (FDTD) is accelerated on a graphics processing unit (GPU) by means of the Compute Unified Device Architecture (CUDA) technology. In the developed implementation of the DGF-FDTD method, a new analytic expression for dyadic DGF derived based on scalar DGF is employed in computations. The DGF-FDTD method on GPU returns solutions that are compatible with the FDTD grid enabling the perfect hybridization of FDTD with the use of time-domain integral equation methods. The correctness of the results of the DGF-FDTD simulations on GPU is verified with the use of the FDTD method executed on a multicore central processing unit (CPU). The developed implementation provides maximally a six-fold speedup relative to the code executed on multicore CPU.

OpenGL accelerated method of the material matrix generation for FDTD simulations

This paper presents the accelerated technique of the material matrix generation from CAD models utilized by the finite-difference time-domain (FDTD) simulators. To achieve high performance of these computations, the parallel-processing power of a graphics processing unit was employed with the use of the OpenGL library. The method was integrated with the developed FDTD solver, providing approximately five-fold speedup of the material matrix generation in comparison to the solution executed on a central processing unit.

Quantitative Analysis of the Human Cornea Using High-speed Swept Source OCT

We present applicability of the high speed swept-source optical coherence tomography for quantitative corneal analysis. The detailed analysis of the influence of eye misalignment, optical distortions or raster density on the corneal topography is presented.