Onsager-Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways

For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system, a path in Cartesian space is transformed into that in Fourier space, and an overdamped Langevin equation is derived for the Fourier components to achieve a canonical ensemble of the path at a finite temperature. To avoid "path trapping" around an initially guessed path, the path sampling method is further combined with a powerful sampling technique, the replica exchange method. The principle and algorithm of our method is numerically demonstrated for a model two-dimensional system with a bifurcated potential landscape. The results are compared with those of conventional transition path sampling and the equilibrium theory, and the error due to path discretization is also discussed.Comment: 20 pages, 5 figures, submitted to J. Chem. Phy

Modern Optimization Algorithms and Applications: Architectural Layout Generation and Parallel Linear Programming

This thesis examines two topics from the field of computational optimization; architectural layout generation and parallel linear programming. The first topic, a modern problem in heuristic optimization, focuses on deriving a general form of the optimization problem and solving it with the proposed Evolutionary Treemap algorithm. Tests of the algorithm\u27s implementation within a highly scalable web application developed with Scala and the web service framework Play reveal the algorithm is effective at generated layouts in multiple styles. The second topic, a classical problem in operations research, focuses on methodologies for implementing the Simplex Algorithm on a parallel computer for solving large-scale linear programming problems. Implementations of the algorithm\u27s data-parallel and task parallel forms illuminate the ideal method for accelerating a solver. The proposed Multi-Path Simplex Algorithm shows an average speed up of over two times that of a popular open-source solver, showing it is an effective methodology for solving linear programming problems

Force balance in canonical ensembles of static granular packings

We investigate the role of local force balance in the transition from a microcanonical ensemble of static granular packings, characterized by an invariant stress, to a canonical ensemble. Packings in two dimensions admit a reciprocal tiling, and a collective effect of force balance is that the area of this tiling is also invariant in a microcanonical ensemble. We present analytical relations between stress, tiling area and tiling area fluctuations, and show that a canonical ensemble can be characterized by an intensive thermodynamic parameter conjugate to one or the other. We test the equivalence of different ensembles through the first canonical simulations of the force network ensemble, a model system.Comment: 9 pages, 9 figures, submitted to JSTA

Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus

The order Picornavirales includes several plant viruses that are currently classified into the families Comoviridae (genera Comovirus, Fabavirus and Nepovirus) and Sequiviridae (genera Sequivirus and Waikavirus) and into the unassigned genera Cheravirus and Sadwavirus. These viruses share properties in common with other picornavirales (particle structure, positive-strand RNA genome with a polyprotein expression strategy, a common replication block including type III helicase, a 3C-like cysteine proteinase and type I RNA-dependent RNA polymerase). However, they also share unique properties that distinguish them from other picornavirales. They infect plants and use specialized proteins or protein domains to move through their host. In phylogenetic analysis based on their replication proteins, these viruses form a separate distinct lineage within the picornavirales branch. To recognize these common properties at the taxonomic level, we propose to create a new family termed “Secoviridae” to include the genera Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus, Sequivirus and Waikavirus. Two newly discovered plant viruses share common properties with members of the proposed family Secoviridae but have distinct specific genomic organizations. In phylogenetic reconstructions, they form a separate sub-branch within the Secoviridae lineage. We propose to create a new genus termed Torradovirus (type species, Tomato torrado virus) and to assign this genus to the proposed family Secoviridae

Sheared force-networks: anisotropies, yielding and geometry

A scenario for yielding of granular matter is presented by considering the ensemble of force networks for a given contact network and applied shear stress $\tau$. As $\tau$ is increased, the probability distribution of contact forces becomes highly anisotropic, the difference between average contact forces along minor and major axis grows, and the allowed networks span a shrinking subspace of all force-networks. Eventually, contacts start to break, and at the yielding shear stress, the packing becomes effectively isostatic. The size of the allowed subspace exhibits simple scaling properties, which lead to a prediction of the yield stress for packings of arbitrary contact number.Comment: 4 pages, 4 figure

Design of Easily Synchronizable Oscillator Networks Using the Monte Carlo Optimization Method

Starting with an initial random network of oscillators with a heterogeneous frequency distribution, its autonomous synchronization ability can be largely improved by appropriately rewiring the links between the elements. Ensembles of synchronization-optimized networks with different connectivities are generated and their statistical properties are studied