An improved moving particle semi-implicit method for dam break simulation

Dam break is quite a common and hazard phenomenon in shipbuilding and ocean engineering. The objective of this study is to investigate dam break hydrodynamics with improved Moving Particle Semi-implicit method (MPS). Compared to traditional mesh methods, MPS is feasible to simulate surface flows with large deformation, however, during the simulation, the pressure oscillates violently, due to misjudgment of surface particles as well as particles gathering together. To modify these problems, a new arc method is applied to judge free surface particles, and a collision model is introduced to avoid particles from gathering together. Hydrostatic pressure is simulated by original and improved MPS. The results verify that improved MPS method is more effective. Based on these, dam break model is investigated with improved MPS

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Determination of the order of phase transitions in Potts model by the graph-weight approach

We examine the order of the phase transition in the Potts model by using the graph representation for the partition function, which allows treating a non-integer number of Potts states. The order of transition is determined by the analysis of the shape of the graph-weight probability distribution. The approach is illustrated on special cases of the one-dimensional Potts model with long-range interactions and on its mean-field limit.Comment: 12 pages LaTeX, 2 eps figures; to be published in Physica

On the well-posedness for the Ideal MHD equations in the Triebel-Lizorkin spaces

In this paper, we prove the local well-posedness for the Ideal MHD equations in the Triebel-Lizorkin spaces and obtain blow-up criterion of smooth solutions. Specially, we fill a gap in a step of the proof of the local well-posedness part for the incompressible Euler equation in \cite{Chae1}.Comment: 16page

The Beale-Kato-Majda criterion to the 3D Magneto-hydrodynamics equations

We study the blow-up criterion of smooth solutions to the 3D MHD equations. By means of the Littlewood-Paley decomposition, we prove a Beale-Kato-Majda type blow-up criterion of smooth solutions via the vorticity of velocity only, i. e. \sup_{j\in\Z}\int_0^T\|\Delta_j(\na\times u)\|_\infty dt, where $\Delta_j$ is a frequency localization on $|\xi|\approx 2^j$.Comment: 12page

Fast Fourier Optimization: Sparsity Matters

Many interesting and fundamentally practical optimization problems, ranging from optics, to signal processing, to radar and acoustics, involve constraints on the Fourier transform of a function. It is well-known that the {\em fast Fourier transform} (fft) is a recursive algorithm that can dramatically improve the efficiency for computing the discrete Fourier transform. However, because it is recursive, it is difficult to embed into a linear optimization problem. In this paper, we explain the main idea behind the fast Fourier transform and show how to adapt it in such a manner as to make it encodable as constraints in an optimization problem. We demonstrate a real-world problem from the field of high-contrast imaging. On this problem, dramatic improvements are translated to an ability to solve problems with a much finer grid of discretized points. As we shall show, in general, the "fast Fourier" version of the optimization constraints produces a larger but sparser constraint matrix and therefore one can think of the fast Fourier transform as a method of sparsifying the constraints in an optimization problem, which is usually a good thing.Comment: 16 pages, 8 figure

Well-posedness of the Ericksen-Leslie system

In this paper, we prove the local well-posedness of the Ericksen-Leslie system, and the global well-posednss for small initial data under the physical constrain condition on the Leslie coefficients, which ensures that the energy of the system is dissipated. Instead of the Ginzburg-Landau approximation, we construct an approximate system with the dissipated energy based on a new formulation of the system.Comment: 16 page

Imaging Synapse Formation during Thymocyte Selection Inability of CD3ζ to Form a Stable Central Accumulation during Negative Selection

AbstractTCR signaling can result in cell fates ranging from activation to tolerance to apoptosis. Organization of molecules in an “immunological synapse” between mature T cells and APCs correlates with the strength of TCR signaling. To investigate synapse formation during thymic selection, we have established a reaggregate system in which molecular recruitment of GFP fusion proteins to thymocyte:stromal cell interfaces can be visualized in real time. We demonstrate that negative selection is associated with efficient conjugate formation and rapid recruitment of p56lck and CD3ζ to an immunological synapse. Interestingly, CD3ζ-GFP does not accumulate at the center of the synapse, as in mature T cells, but at the periphery across a wide range of ligand densities. This implicates differences in synapse geometry in initiation of alternate signals downstream of the TCR

Local minimal energy landscapes in river networks

The existence and stability of the universality class associated to local minimal energy landscapes is investigated. Using extensive numerical simulations, we first study the dependence on a parameter $\gamma$ of a partial differential equation which was proposed to describe the evolution of a rugged landscape toward a local minimum of the dissipated energy. We then compare the results with those obtained by an evolution scheme based on a variational principle (the optimal channel networks). It is found that both models yield qualitatively similar river patterns and similar dependence on $\gamma$. The aggregation mechanism is however strongly dependent on the value of $\gamma$. A careful analysis suggests that scaling behaviors may weakly depend both on $\gamma$ and on initial condition, but in all cases it is within observational data predictions. Consequences of our resultsComment: 12 pages, 13 figures, revtex+epsfig style, to appear in Phys. Rev. E (Nov. 2000