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

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

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

The tail of the contact force distribution in static granular materials

We numerically study the distribution P(f) of contact forces in frictionless bead packs, by averaging over the ensemble of all possible force network configurations. We resort to umbrella sampling to resolve the asymptotic decay of P(f) for large f, and determine P(f) down to values of order 10^{-45} for ordered and disordered systems in two and three dimensions. Our findings unambiguously show that, in the ensemble approach, the force distributions decay much faster than exponentially: P(f) ~ exp(-f^{\alpha}), with alpha \approx 2.0 for 2D systems, and alpha \approx 1.7 for 3D systems.Comment: 4 pages, 4 figures, submitted to Phys. Rev.

Single Chain Force Spectroscopy: Sequence Dependence

We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe local minima on the path of stretching and releasing. At given force, we find multiple configurations which are separated by energy barriers. A collapsed globular configuration consists of several domains which unravel cooperatively. Upon stretching, unfolding path shows stepwise pattern corresponding to the unfolding of each domain. While releasing, several cores can be created simultaneously in the middle of the chain resulting in a different path of collapse.Comment: 6 pages 3 figure