Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

From the Publisher: 
The accessible presentation of this book gives both a general view of the entire computer vision enterprise and also offers sufficient detail to be able to build useful applications. Users learn techniques that have proven to be useful by first-hand experience and a wide range of mathematical methods. A CD-ROM with every copy of the text contains source code for programming practice, color images, and illustrative movies. Comprehensive and up-to-date, this book includes essential topics that either reflect practical significance or are of theoretical importance. Topics are discussed in substantial and increasing depth. Application surveys describe numerous important application areas such as image based rendering and digital libraries. Many important algorithms broken down and illustrated in pseudo code. Appropriate for use by engineers as a comprehensive reference to the computer vision enterprise.

Computer vision : a modern approach = 计算机视觉 : 一种现代的方法

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Physical Review B

(b) Write out the equations for the time dependence of ρ11, ρ22, ρ12 and ρ21 assuming that a light field interaction V = -μ12Ee iωt + c.c. couples only levels |1> and |2>, and that the excited levels exhibit spontaneous decay. (8 marks) (c) Under steady-state conditions, find the ratio of populations in states |2> and |3>. (3 marks) (d) Find the slowly varying amplitude ̃ ρ 12 of the polarization ρ12 = ̃ ρ 12e iωt . (6 marks) (e) In the limiting case that no decay is possible from intermediate level |3>, what is the ground state population ρ11(∞)? (2 marks) 2. (15 marks total) In a 2-level atom system subjected to a strong field, dressed states are created in the form |D1(n)> = sin θ |1,n> + cos θ |2,n-1> |D2(n)> = cos θ |1,n> sin θ |2,n-1>

The Quantum Theory of Light

The concept of permeability of porous media is discussed, and a modification of Kozeny's permeability equation to include the effect of effective porosity is introduced. An analytical expression for the specific surface area of a system constructed of randomly placed identical obstacles with unrestricted overlap is derived, and a lattice-gas cellular automaton method is then used to simulate the dependence on porosity of permeability, tortuosity, and effective porosity for a flow of Newtonian uncompressible fluid in this two-dimensional porous substance. The simulated permeabilities can well be explained by the concept of effective porosity, and the exact form of the specific surface area. The critical exponent of the permeability near the percolation threshold is also determined from the simulations.

Permeability and effective porosity of porous media

The concept of tortuosity of fluid flow in porous media is discussed. A lattice-gas cellular automaton method is applied to solve the flow of a Newtonian uncompressible fluid in a two-dimensional porous substance constructed by randomly placed rectangles of equal size and with unrestricted overlap. A clear correlation between the average tortuosity of the flow paths and the porosity of the substance has been found. \textcopyright{} 1996 The American Physical Society.

Tortuous flow in porous media

Numerical micropermeametry is performed on three-dimensional porous samples having a linear size of approximately 3 mm and a resolution of 75 microm One of the samples is a microtomographic image of Fontainebleau sandstone Two of the samples are stochastic reconstructions with the same porosity, specific surface area, and two-point correlation function as the Fontainebleau sample The fourth sample is a physical model that mimics the processes of sedimentation, compaction, and diagenesis of Fontainebleau sandstone The permeabilities of these samples are determined by numerically solving at low Reynolds numbers the appropriate Stokes equations in the pore spaces of the samples The physical diagenesis model appears to reproduce the permeability of the real sandstone sample quite accurately, while the permeabilities of the stochastic reconstructions deviate from the latter by at least an order of magnitude This finding confirms earlier qualitative predictions based on local porosity theory Two numerical algorithms were used in these simulations One is based on the lattice-Boltzmann method, and the other on conventional finite-difference techniques The accuracy of these two methods is discussed and compared, also with experiment

Lattice-Boltzmann and finite-difference simulations for the permeability for three-dimensional porous media.

Existing ultrasound devices for assessing the human tibia are based on detecting the first arriving signal, corresponding to a wave propagating at, or close to, the bulk longitudinal velocity in bone. However, human long bones are effectively irregular hollow tubes and should theoretically support the propagation of more complex guided modes similar to Lamb waves in plates. Guided waves are attractive because they propagate throughout the bone thickness and can potentially yield more information on bone material properties and architecture. In this study, Lamb wave theory and numerical simulations of wave propagation were used to gain insights into the expected behaviour of guided waves in bone. Experimental measurements in acrylic plates, using a prototype low-frequency axial pulse transmission device, confirmed the presence of two distinct propagating waves: the first arriving wave propagating at, or close to, the longitudinal velocity, and a slower second wave whose behaviour was consistent with the lowest order Lamb antisymmetrical (A0) mode. In a pilot study of healthy and osteoporotic subjects, the velocity of the second wave differed significantly between the two groups, whereas the first arriving wave velocity did not, suggesting the former to be a more sensitive indicator of osteoporosis. We conclude that guided wave measurements may offer an enhanced approach to the ultrasonic characterization of long bones.

https://iopscience.iop.org/article/10.1088/0967-3334/23/4/313/pdf

Guided ultrasonic waves in long bones: modelling, experiment and in vivo application

We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribution of a non-binding fluorescent protein. Distinction can now be made within this method between diffusion in the liquid phase of the cell (cytosol/nucleosol) and the cytoplasm/nucleoplasm. Here we applied the method to analyze fluorescence recovery after photobleach (FRAP) experiments in which the diffusion coefficient of a freely-diffusing model protein was determined for two different cell lines, and to explain the clear difference typically observed between conventional FRAP results and those of fluorescence correlation spectroscopy (FCS). A large difference was found in the FRAP experiments between diffusion in the cytoplasm/nucleoplasm and in the cytosol/nucleosol, for all of which the diffusion coefficients were determined. The cytosol results were found to be in very good agreement with those by FCS.

/pdf/protein-diffusion-in-mammalian-cell-cytoplasm-3wbv5kpwa2.pdf

Jussi Timonen

Papers

Permeability and effective porosity of porous media

Tortuous flow in porous media

Lattice-Boltzmann and finite-difference simulations for the permeability for three-dimensional porous media.

Guided ultrasonic waves in long bones: modelling, experiment and in vivo application

Protein diffusion in mammalian cell cytoplasm.