Physics Commons^™

Highly Efficient And Exact Method For Parallelization Of Grid-Based Algorithms And Its Implementation In Delphi, Chuan Li, Lin Li, Jie Zhang, Emil Alexov

Publications

The Gauss–Seidel (GS) method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the GS method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here, we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of processes or computing units. In …

Effects Of Long-Range Tip-Sample Interaction On Magnetic Force Imaging: A Comparative Study Between Bimorph Driven System And Electrostatic Force Modulation, Byung I. Kim

Physics Faculty Publications and Presentations

Magnetic force microscopy (MFM) using electrostatic force modulation has been designed and developed to avoid the drawbacks of the bimorph driven system. The bimorph driven system has poor frequency response and overlap of the topographic features on magnetic structures of the MFM images. In the electrostatic force modulation system, the amplitude increases in the noncontact regime as the tip approaches due to the capacitive coupling between tip and sample. MFM using electrostatic force modulation has been applied to observe maze-like stripe domain structures on a CoCr film. The contrast mechanism and imaging stability of MFM using electrostatic force modulation are …

Delphi: A Comprehensive Suite For Delphi Software And Associated Resources, Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov

Publications

Background

Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.

Results

Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding …

Conformational Temperature-Dependent Behavior Of A Histone H2ax: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials, Miriam Fritsche, Ras B. Pandey, Barry L. Farmer, Dieter W. Heerman

Faculty Publications

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input …