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Small System (small + system)
Selected AbstractsA spatially explicit study of prey,predator interactions in larval fish: assessing the influence of food and predator abundance on larval growth and survivalFISHERIES OCEANOGRAPHY, Issue 1 2003P. Pepin Abstract We apply a coupled biophysical model to reconstruct the environmental history of larval radiated shanny in Conception Bay, Newfoundland. Data on the larvae, their prey and predators were collected during a 2-week period. Our goal was to determine whether environmentally explicit information could be used to infer the characteristics of individual larvae that are most likely to survive. Backward drift reconstruction was used to assess the influence of variations in the feeding environment on changes in the growth rates of individual larvae. Forward drift projections were used to assess the impact of predators on mortality rates as well as the cumulative density distribution of growth rates in the population of larvae in different areas of the bay. There was relatively little influence of current feeding conditions on increment widths. Patterns of selective mortality indicate that fast-growing individuals suffered higher mortality rates, suggesting they were growing into a predator's prey field. However, the mortality rates appeared to increase with decreasing predator abundance, based on the drift reconstructions. The relationship of growth and mortality with environmental conditions suggests that short-term, small-scale variations in environmental history may be difficult to describe accurately in this relatively small system (,1000 km2). [source] A level set-based immersed interface method for solving incompressible viscous flows with the prescribed velocity at the boundaryINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 3 2010Zhijun Tan Abstract A second-order accurate immersed interface method (IIM) is presented for solving the incompressible Navier,Stokes equations with the prescribed velocity at the boundary, which is an extension of the IIM of Le et al. (J. Comput. Phys. 2006; 220:109,138) to a level set representation of the boundary in place of the Lagrangian representation of the boundary using control points on a uniform Cartesian grid. In order to enforce the prescribed velocity boundary condition, the singular forces at the immersed boundary are applied on the fluid. These forces are related to the jump in pressure and the jumps in the derivatives of both the pressure and velocity, and are approximated via using the local Hermite cubic spline interpolation. The strength of singular forces is determined by solving a small system of equations at each time step. The Navier,Stokes equations are discretized via using finite difference method with the incorporation of jump conditions on a staggered Cartesian grid and solved by a second-order accurate projection method. Numerical results demonstrate the accuracy and ability of the proposed method to simulate the viscous flows in irregular domains. Copyright © 2009 John Wiley & Sons, Ltd. [source] Parallel Fock matrix construction with distributed shared memory model for the FMO-MO methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2010Hiroaki Umeda Abstract A parallel Fock matrix construction program for FMO-MO method has been developed with the distributed shared memory model. To construct a large-sized Fock matrix during FMO-MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO-MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6-31G level of theory, with the frontier orbitals being extracted by a Sakurai-Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen-components on a PC cluster system using 256 processors. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Efficiency of nested Markov chain Monte Carlo for polarizable potentials and perturbed HamiltoniansINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Florent Calvo Abstract Nested Markov chain Monte Carlo is a rigorous way to enhance sampling of a given energy landscape using an auxiliary, approximate potential energy surface. Its practical efficiency mainly depends on how cheap and how different are the auxiliary potential with respect to the reference system. In this article, a combined efficiency index is proposed and assessed for two important families of energy surfaces. As illustrated for water clusters, many-body polarizable potentials can be approximated by simplifying the polarization contribution and keeping only the two-body terms. In small systems, neglecting polarization entirely is also acceptable. When the reference potential energy is obtained from diagonalization of a quantum mechanical Hamiltonian, a first-order perturbation scheme can be used to estimate the energy difference occuring on a Monte Carlo move. Our results indicate that this perturbation approximation performs well provided that the number of steps between successive diagonalization is adjusted beforehand. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2342,2346, 2010 [source] Robustness of efficient server assignment policies to service time distributions in finite-buffered linesNAVAL RESEARCH LOGISTICS: AN INTERNATIONAL JOURNAL, Issue 6 2010Eser K, zlar Abstract We study the assignment of flexible servers to stations in tandem lines with service times that are not necessarily exponentially distributed. Our goal is to achieve optimal or near-optimal throughput. For systems with infinite buffers, it is already known that the effective assignment of flexible servers is robust to the service time distributions. We provide analytical results for small systems and numerical results for larger systems that support the same conclusion for tandem lines with finite buffers. In the process, we propose server assignment heuristics that perform well for systems with different service time distributions. Our research suggests that policies known to be optimal or near-optimal for Markovian systems are also likely to be effective when used to assign servers to tasks in non-Markovian systems. © 2010 Wiley Periodicals, Inc. Naval Research Logistics, 2010 [source] Differential dye coupling reveals lateral giant escape circuit in crayfishTHE JOURNAL OF COMPARATIVE NEUROLOGY, Issue 1 2003Brian L. Antonsen Abstract The lateral giant (LG) escape circuit of crayfish mediates a coordinated escape triggered by strong attack to the abdomen. The LG circuit is one of the best understood of small systems, but models of the circuit have mostly been limited to simple ball-and-stick representations, which ignore anatomical details of contacts between circuit elements. Many of the these contacts are electrical; here we use differential dye coupling, a technique which could help reveal connection patterns in many neural circuits, to reveal in detail the circuit within the terminal abdominal ganglion. Sensory input from the tailfan forms a somatotopic map on the projecting LG dendrites, which together with interafferent coupling mediates a lateral excitatory network that selectively amplifies strong, phasic, converging input to LG. Mechanosensory interneurons contact LG at sites distinct from the primary afferents and so maximize their summated effect on LG. Motor neurons and premotor interneurons are excited near the initial segments of the LGs and innervate muscles for generating uropod flaring and telson flexion. Previous research has shown that spatial patterns of input are important for signal integration in LG; this map of electrical contact points will help us to understand synaptic processing in this system. J. Comp. Neurol. 466:1,13, 2003. © 2003 Wiley-Liss, Inc. [source] | ||||||||||