Rigidity of Orientationally Ordered Domains of Short Chain Molecules

By molecular dynamics simulation, discovered is a strange rigid-like nature for a hexagonally packed domain of short chain molecules. In spite of the non-bonded short-range interaction potential (Lennard-Jones potential) among chain molecules, the packed domain gives rise to a resultant global moment of inertia. Accordingly, as two domains encounter obliquely, they rotate so as to be parallel to each other keeping their overall structures as if they were rigid bodies.Comment: 7 pages, 5 figures, and 2 table

Algorithm for numerical integration of the rigid-body equations of motion

A new algorithm for numerical integration of the rigid-body equations of motion is proposed. The algorithm uses the leapfrog scheme and the quantities involved are angular velocities and orientational variables which can be expressed in terms of either principal axes or quaternions. Due to specific features of the algorithm, orthonormality and unit norms of the orientational variables are integrals of motion, despite an approximate character of the produced trajectories. It is shown that the method presented appears to be the most efficient among all known algorithms of such a kind.Comment: 4 pages, 1 figur

Atomistic mechanisms for the ordered growth of Co nano-dots on Au(788): comparison of VT-STM experiments and multi-scaled calculations

Hetero-epitaxial growth on a strain-relief vicinal patterned substrate has revealed unprecedented 2D long range ordered growth of uniform cobalt nanostructures. The morphology of a Co sub-monolayer deposit on a Au(111) reconstructed vicinal surface is analyzed by Variable Temperature Scanning Tunneling Microscopy (VT-STM) experiments. A rectangular array of nano-dots (3.8 nm x 7.2 nm) is found for a particularly large deposit temperature range lying from 60 K to 300 K. Although the nanodot lattice is stable at room temperature, this paper focus on the early stage of ordered nucleation and growth at temperatures between 35 K and 480 K. The atomistic mechanisms leading to the nanodots array are elucidated by comparing statistical analysis of VT-STM images with multi-scaled numerical calculations combining both Molecular Dynamics for the quantitative determination of the activation energies for the atomic motion and the Kinetic Monte Carlo method for the simulations of the mesoscopic time and scale evolution of the Co submonolayer

Dynamical Properties and Plasmon Dispersion of a Weakly Degenerate Correlated One-Component Plasma

Classical Molecular Dynamics (MD) simulations for a one-component plasma (OCP) are presented. Quantum effects are included in the form of the Kelbg potential. Results for the dynamical structure factor are compared with the Vlasov and RPA (random phase approximation) theories. The influence of the coupling parameter $\Gamma$, degeneracy parameter $\rho \Lambda^3$ and the form of the pair interaction on the optical plasmon dispersion is investigated. An improved analytical approximation for the dispersion of Langmuir waves is presented.Comment: 23 pages, includes 7 ps/eps-figures and 2 table

Discovery of Bright Galactic R Coronae Borealis and DY Persei Variables: Rare Gems Mined from ACVS

We present the results of a machine-learning (ML) based search for new R Coronae Borealis (RCB) stars and DY Persei-like stars (DYPers) in the Galaxy using cataloged light curves from the All-Sky Automated Survey (ASAS) Catalog of Variable Stars (ACVS). RCB stars - a rare class of hydrogen-deficient carbon-rich supergiants - are of great interest owing to the insights they can provide on the late stages of stellar evolution. DYPers are possibly the low-temperature, low-luminosity analogs to the RCB phenomenon, though additional examples are needed to fully establish this connection. While RCB stars and DYPers are traditionally identified by epochs of extreme dimming that occur without regularity, the ML search framework more fully captures the richness and diversity of their photometric behavior. We demonstrate that our ML method can use newly discovered RCB stars to identify additional candidates within the same data set. Our search yields 15 candidates that we consider likely RCB stars/DYPers: new spectroscopic observations confirm that four of these candidates are RCB stars and four are DYPers. Our discovery of four new DYPers increases the number of known Galactic DYPers from two to six; noteworthy is that one of the new DYPers has a measured parallax and is m ~ 7 mag, making it the brightest known DYPer to date. Future observations of these new DYPers should prove instrumental in establishing the RCB connection. We consider these results, derived from a machine-learned probabilistic classification catalog, as an important proof-of-concept for the efficient discovery of rare sources with time-domain surveys.Comment: 18 pages, 2 new figures, accepted for publication in Ap

Elaborating Transition Interface Sampling Methods

We review two recently developed efficient methods for calculating rate constants of processes dominated by rare events in high-dimensional complex systems. The first is transition interface sampling (TIS), based on the measurement of effective fluxes through hypersurfaces in phase space. TIS improves efficiency with respect to standard transition path sampling (TPS) rate constant techniques, because it allows a variable path length and is less sensitive to recrossings. The second method is the partial path version of TIS. Developed for diffusive processes, it exploits the loss of long time correlation. We discuss the relation between the new techniques and the standard reactive flux methods in detail. Path sampling algorithms can suffer from ergodicity problems, and we introduce several new techniques to alleviate these problems, notably path swapping, stochastic configurational bias Monte Carlo shooting moves and order-parameter free path sampling. In addition, we give algorithms to calculate other interesting properties from path ensembles besides rate constants, such as activation energies and reaction mechanisms.Comment: 36 pages, 5 figure

The Dutchman Vol. 6, No. 1

● Editorial ● Somerset County Decorated Barns ● Butter Molds ● Restaurants, too, Go Dutch ● The Hostetter Fractur Collection ● Bindnagle\u27s Church ● The Harry S. High Folk Art Collection ● Lebanon Valley Date Stones ● Of Bells and Bell Towers ● John Durang, the First Native American Dancer ● Stoffel Rilbps\u27 Epistle ● The First Singing of Our National Anthem ● Pennsylvania Dutch Pioneershttps://digitalcommons.ursinus.edu/dutchmanmag/1000/thumbnail.jp

Atomic-scale modeling of the deformation of nanocrystalline metals

Nanocrystalline metals, i.e. metals with grain sizes from 5 to 50 nm, display technologically interesting properties, such as dramatically increased hardness, increasing with decreasing grain size. Due to the small grain size, direct atomic-scale simulations of plastic deformation of these materials are possible, as such a polycrystalline system can be modeled with the computational resources available today. We present molecular dynamics simulations of nanocrystalline copper with grain sizes up to 13 nm. Two different deformation mechanisms are active, one is deformation through the motion of dislocations, the other is sliding in the grain boundaries. At the grain sizes studied here the latter dominates, leading to a softening as the grain size is reduced. This implies that there is an ``optimal'' grain size, where the hardness is maximal. Since the grain boundaries participate actively in the deformation, it is interesting to study the effects of introducing impurity atoms in the grain boundaries. We study how silver atoms in the grain boundaries influence the mechanical properties of nanocrystalline copper.Comment: 10 pages, LaTeX2e, PS figures and sty files included. To appear in Mater. Res. Soc. Symp. Proc. vol 538 (invited paper). For related papers, see http://www.fysik.dtu.dk/~schiotz/publist.htm

Spontaneous alloying in binary metal microclusters - A molecular dynamics study -

Microcanonical molecular dynamics study of the spontaneous alloying(SA), which is a manifestation of fast atomic diffusion in a nano-sized metal cluster, is done in terms of a simple two dimensional binary Morse model. Important features observed by Yasuda and Mori are well reproduced in our simulation. The temperature dependence and size dependence of the SA phenomena are extensively explored by examining long time dynamics. The dominant role of negative heat of solution in completing the SA is also discussed. We point out that a presence of melting surface induces the diffusion of core atoms even if they are solid-like. In other words, the {\it surface melting} at substantially low temperature plays a key role in attaining the SA.Comment: 15 pages, 12 fgures, Submitted to Phys.Rev.

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers are, how the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times or rate constants, and the hierarchical relationship among basins, complete the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, the dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press