Density-based cluster algorithms for the identification of core sets

The core-set approach is a discretization method for Markov state models of complex molecular dynamics. Core-sets are disjoint metastable regions in the conformational space, which need to be known prior to the construction of the core-set model. We propose to use density-based cluster algorithms to identify the cores. We compare three different density-based cluster algorithms: the CNN, the DBSCAN and theJarvis-Patrick algorithm. While the core-set models based on the CNN and DBSCAN clustering are well-converged, constructing core-models based on the Jarvis-Patrick clustering cannot be recommended. In a well-converged core-set model, the number of core sets is up to an order of magnitude smaller than the number of states in a conventional Markov state model with comparable approximation error. Moreover, using the density-based clustering one can extend the core-set method to systems which are not strongly metastable. This is important for the practical application of the core-set method because most biologically interesting systems are only marginally metastable. The key point is to perform a hierarchical density-based clustering while monitoring the structure of metric matrix which appears in the core-set method. We test this approach on a molecular-dynamics simulation of a highly exible 14-residue peptide. The resulting core-set models have a high spatial resolution and can distinguish between conformationally similar yet chemically different structures, such as register-shifted hairpin structures

Girsanov reweighting for path ensembles and Markov state models

The sensitivity of molecular dynamics on changes in the potential energy function plays an important role in understanding the dynamics and function of complex molecules. We present a method to obtain path ensemble averages of a perturbed dynamics from a set of paths generated by a reference dynamics. It is based on the concept of path probability measure and the Girsanov theorem, a result from stochastic analysis to estimate a change of measure of a path ensemble. Since Markov state models (MSM) of the molecular dynamics can be formulated as a combined phasespace and path ensemble average, the method can be extended to reweight MSMs by combining it with a reweighting of the Boltzmann distribution. We demonstrate how to efficiently implement the Girsanov reweighting in a molecular dynamics simulation program by calculating parts of the reweighting factor "on the fly" during the simulation, and we benchmark the method on test systems ranging from a two-dimensional diffusion process to an artificial many-body system and alanine dipeptide and valine dipeptide in implicit and explicit water. The method can be used to study the sensitivity of molecular dynamics on external perturbations as well as to reweight trajectories generated by enhanced sampling schemes to the original dynamics

An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates

In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov’s theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a nonequilibrium dynamics which is used to sample the equilibrium quantities

Direct and indirect genetic effects of a social supergene.

Indirect genetic effects describe phenotypic variation that results from differences in the genotypic composition of social partners. Such effects represent heritable sources of environmental variation in eusocial organisms because individuals are typically reared by their siblings. In the fire ant Solenopsis invicta, a social supergene exhibits striking indirect genetic effects on worker regulation of colony queen number, such that the genotypic composition of workers at the supergene determines whether colonies contain a single or multiple queens. We assessed the direct and indirect genetic effects of this supergene on gene expression in brains and abdominal tissues from laboratory-reared workers and compared these with previously published data from field-collected prereproductive queens. We found that direct genetic effects caused larger gene expression changes and were more consistent across tissue types and castes than indirect genetic effects. Indirect genetic effects influenced the expression of many loci but were generally restricted to the abdominal tissues. Further, indirect genetic effects were only detected when the genotypic composition of social partners differed throughout the development and adult life of focal workers, and were often only significant with relatively lenient statistical cutoffs. Our study provides insight into direct and indirect genetic effects of a social supergene on gene regulatory dynamics across tissues and castes in a complex society

Fission Hindrance in hot 216Th: Evaporation Residue Measurements

The fusion evaporation-residue cross section for 32S+184W has been measured at beam energies of E_beam = 165, 174, 185, 196, 205, 215, 225, 236, 246,and 257 MeV using the ATLAS Fragment Mass Analyzer. The data are compared with Statistical Model calculations and it is found that a nuclear dissipation strength, which increases with excitation energy, is required to reproduce the excitation function. A comparison with previously published data show that the dissipation strength depends strongly on the shell structure of the nuclear system.Comment: 15 pages 9 figure

Antiferromagnetic Domains and Superconductivity in UPt3

We explore the response of an unconventional superconductor to spatially inhomogeneous antiferromagnetism (SIAFM). Symmetry allows the superconducting order parameter in the E-representation models for UPt3 to couple directly to the AFM order parameter. The Ginzburg-Landau equations for coupled superconductivity and SIAFM are solved numerically for two possible SIAFM configurations: (I) abutting antiferromagnetic domains of uniform size, and (II) quenched random disorder of `nanodomains' in a uniform AFM background. We discuss the contributions to the free energy, specific heat, and order parameter for these models. Neither model provides a satisfactory account of experiment, but results from the two models differ significantly. Our results demonstrate that the response of an E_{2u} superconductor to SIAFM is strongly dependent on the spatial dependence of AFM order; no conclusion can be drawn regarding the compatibility of E_{2u} superconductivity with UPt3 that is independent of assumptions on the spatial dependence of AFMComment: 12 pages, 13 figures, to appear in Phys. Rev.

Differential cross section and recoil polarization measurements for the gamma p to K+ Lambda reaction using CLAS at Jefferson Lab

We present measurements of the differential cross section and Lambda recoil polarization for the gamma p to K+ Lambda reaction made using the CLAS detector at Jefferson Lab. These measurements cover the center-of-mass energy range from 1.62 to 2.84 GeV and a wide range of center-of-mass K+ production angles. Independent analyses were performed using the K+ p pi- and K+ p (missing pi -) final-state topologies; results from these analyses were found to exhibit good agreement. These differential cross section measurements show excellent agreement with previous CLAS and LEPS results and offer increased precision and a 300 MeV increase in energy coverage. The recoil polarization data agree well with previous results and offer a large increase in precision and a 500 MeV extension in energy range. The increased center-of-mass energy range that these data represent will allow for independent study of non-resonant K+ Lambda photoproduction mechanisms at all production angles.Comment: 22 pages, 16 figure

Coherent Photoproduction of pi^+ from 3^He

We have measured the differential cross section for the $\gamma$$^3$He$\rightarrow \pi^+ t$ reaction. This reaction was studied using the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. Real photons produced with the Hall-B bremsstrahlung tagging system in the energy range from 0.50 to 1.55 GeV were incident on a cryogenic liquid $^3$He target. The differential cross sections for the $\gamma$$^3$He$\rightarrow \pi^+ t$ reaction were measured as a function of photon-beam energy and pion-scattering angle. Theoretical predictions to date cannot explain the large cross sections except at backward angles, showing that additional components must be added to the model.Comment: 11 pages, 16 figure

First-level trigger systems for LHC experiments

We propose to carry out a broad-based programme of R&D on level-1 trigger systems for LHC experiments. We will consider the overall level-1 which coordinates different subtriggers and which interacts with the front end electronics and with the level-2 system. Careful attention will be paid to systems aspects and problems of synchronization within the pipelined processor system. Trigger algorithms for selecting events with high-pt electrons, photons, muons, jets and large missing Et will be evaluated by physics simulation studies. We will study possible implementations of such trigger algorithms in fast electronics by making conceptual design studies and using behavioural simulation models. For critical areas more detailed design studies will be made, and prototypes of some key elements will be constructed and tested. The proposed R&D project builds on existing studies and will complement other R&D projects already funded by the DRDC

North American Prairie Wetlands are Important Nonforested Land-Based Carbon Storage Sites

We evaluated the potential of prairie wetlands in North America as carbon sinks. Agricultural conversion has resulted in the average loss of 10.1 Mg ha- of soil organic carbon on over 16 million ha of wetlands in this region. Wetland restoration has potential to sequester 378 Tg of organic carbon over a 10-year period. Wetlands can sequester over twice the organic carbon as no-till cropland on only about 17% of the total land area in the region. We estimate that wetland restoration has potential to offset 2.4% of the annual fossil CO2 emission reported for North America in 1990