UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models

UMass Morph Server (UMMS) has been developed for the broad impact on the study of molecular dynamics (MD). The elastic network model (ENM) of a given macromolecule has been proven as a useful tool for analyzing thermal behaviors locally and predicting folding pathways globally. UMMS utilizes coarse-grained ENMs at various levels. These simplifications remarkably save computation time compared with all-atom MD simulations so that one can bring down massive computational problems from a supercomputer to a PC. To improve computational efficiency and physical reality of ENMs, the symmetry-constrained, rigid-cluster, hybrid and chemical-bond ENMs have been developed and implemented at UMMS. One can request both harmonic normal mode analysis of a single macromolecule and anharmonic pathway generation between two conformations of a same molecule using elastic network interpolation at

Production and optical properties of liquid scintillator for the JSNS2^{2} experiment

The JSNS$^{2}$ (J-PARC Sterile Neutrino Search at J-PARC Spallation Neutron Source) experiment will search for neutrino oscillations over a 24 m short baseline at J-PARC. The JSNS$^{2}$ inner detector will be filled with 17 tons of gadolinium-loaded liquid scintillator (LS) with an additional 31 tons of unloaded LS in the intermediate $\gamma$-catcher and outer veto volumes. JSNS$^{2}$ has chosen Linear Alkyl Benzene (LAB) as an organic solvent because of its chemical properties. The unloaded LS was produced at a refurbished facility, originally used for scintillator production by the RENO experiment. JSNS$^{2}$ plans to use ISO tanks for the storage and transportation of the LS. In this paper, we describe the LS production, and present measurements of its optical properties and long term stability. Our measurements show that storing the LS in ISO tanks does not result in degradation of its optical properties.Comment: 7 pages, 4 figures

Development of Auto Scaling Method for 3D Rock Fragmentation Measurement System

Fragmentation Distribution is one of the important aspects of mining operations as it affects productivities on the majority of Mine-to-Mill operations. Nevertheless the significance of fragmentation management, the mining industry has relied on 2D image based fragmentation measurement system which poses many downsides. To overcome the drawbacks of current 2D fragmentation measurement system, 3D Rock Fragmentation Measurement System has been proposed with using 3D photogrammetry technologies. One of the common difficulty of fragmentation measurement system is scaling of the object, which is an essential component to secure the accuracy of particle size distribution. In this study, the actual scales and size information of objects have been obtained by measuring the acceleration when moving between the photographing points and giving the information of the distance obtained from the acceleration. The developed system would be equipped with the 3D Rock Fragmentation Measurement System

Robust Upward Dispersion of the Neutron Spin Resonance in the Heavy Fermion Superconductor Ce1−x_{1-x}Ybx_{x}CoIn5_5

The neutron spin resonance is a collective magnetic excitation that appears in copper oxide, iron pnictide, and heavy fermion unconventional superconductors. Although the resonance is commonly associated with a spin-exciton due to the $d$($s^{\pm}$)-wave symmetry of the superconducting order parameter, it has also been proposed to be a magnon-like excitation appearing in the superconducting state. Here we use inelastic neutron scattering to demonstrate that the resonance in the heavy fermion superconductor Ce$_{1-x}$Yb$_{x}$CoIn$_5$ with $x=0,0.05,0.3$ has a ring-like upward dispersion that is robust against Yb-doping. By comparing our experimental data with random phase approximation calculation using the electronic structure and the momentum dependence of the $d_{x^2-y^2}$-wave superconducting gap determined from scanning tunneling microscopy for CeCoIn$_5$, we conclude the robust upward dispersing resonance mode in Ce$_{1-x}$Yb$_{x}$CoIn$_5$ is inconsistent with the downward dispersion predicted within the spin-exciton scenario.Comment: Supplementary Information available upon reques

Hamiltonian Analysis of Poincar\'e Gauge Theory: Higher Spin Modes

We examine several higher spin modes of the Poincar\'e gauge theory (PGT) of gravity using the Hamiltonian analysis. The appearance of certain undesirable effects due to non-linear constraints in the Hamiltonian analysis are used as a test. We find that the phenomena of field activation and constraint bifurcation both exist in the pure spin 1 and the pure spin 2 modes. The coupled spin-$0^-$ and spin-$2^-$ modes also fail our test due to the appearance of constraint bifurcation. The ``promising'' case in the linearized theory of PGT given by Kuhfuss and Nitsch (KRNJ86) likewise does not pass. From this analysis of these specific PGT modes we conclude that an examination of such nonlinear constraint effects shows great promise as a strong test for this and other alternate theories of gravity.Comment: 30 pages, submitted to Int. J. Mod. Phys.