Robust Parameter Selection for Parallel Tempering

This paper describes an algorithm for selecting parameter values (e.g. temperature values) at which to measure equilibrium properties with Parallel Tempering Monte Carlo simulation. Simple approaches to choosing parameter values can lead to poor equilibration of the simulation, especially for Ising spin systems that undergo $1^st$-order phase transitions. However, starting from an initial set of parameter values, the careful, iterative respacing of these values based on results with the previous set of values greatly improves equilibration. Example spin systems presented here appear in the context of Quantum Monte Carlo.Comment: Accepted in International Journal of Modern Physics C 2010, http://www.worldscinet.com/ijmp

Importance of Explicit Vectorization for CPU and GPU Software Performance

Much of the current focus in high-performance computing is on multi-threading, multi-computing, and graphics processing unit (GPU) computing. However, vectorization and non-parallel optimization techniques, which can often be employed additionally, are less frequently discussed. In this paper, we present an analysis of several optimizations done on both central processing unit (CPU) and GPU implementations of a particular computationally intensive Metropolis Monte Carlo algorithm. Explicit vectorization on the CPU and the equivalent, explicit memory coalescing, on the GPU are found to be critical to achieving good performance of this algorithm in both environments. The fully-optimized CPU version achieves a 9x to 12x speedup over the original CPU version, in addition to speedup from multi-threading. This is 2x faster than the fully-optimized GPU version.Comment: 17 pages, 17 figure

Minimum Cost Homomorphisms to Locally Semicomplete and Quasi-Transitive Digraphs

For digraphs $G$ and $H$, a homomorphism of $G$ to $H$ is a mapping $f:\ V(G)\dom V(H)$such that$uv\in A(G)$implies$f(u)f(v)\in A(H)$. If, moreover, each vertex$u \in V(G)$is associated with costs$c_i(u), i \in V(H)$, then the cost of a homomorphism$f$is$\sum_{u\in V(G)}c_{f(u)}(u)$. For each fixed digraph$H$, the minimum cost homomorphism problem for$H$, denoted MinHOM($H$), can be formulated as follows: Given an input digraph$G$, together with costs$c_i(u)$,$u\in V(G)$,$i\in V(H)$, decide whether there exists a homomorphism of$G$to$H$ and, if one exists, to find one of minimum cost. Minimum cost homomorphism problems encompass (or are related to) many well studied optimization problems such as the minimum cost chromatic partition and repair analysis problems. We focus on the minimum cost homomorphism problem for locally semicomplete digraphs and quasi-transitive digraphs which are two well-known generalizations of tournaments. Using graph-theoretic characterization results for the two digraph classes, we obtain a full dichotomy classification of the complexity of minimum cost homomorphism problems for both classes

LOCV calculations for polarized liquid 3He^3{He} with the spin-dependent correlation

We have used the lowest order constrained variational (LOCV) method to calculate some ground state properties of polarized liquid $^{3}He$ at zero temperature with the spin-dependent correlation function employing the Lennard-Jones and Aziz pair potentials. We have seen that the total energy of polarized liquid $^{3}He$ increases by increasing polarization. For all polarizations, it is shown that the total energy in the spin-dependent case is lower than the spin-independent case. We have seen that the difference between the energies of spin-dependent and spin-independent cases decreases by increasing polarization. We have shown that the main contribution of the potential energy comes from the spin-triplet state.Comment: 14 pages, 5 figures. Int. J. Mod. Phys. B (2008) in pres

Lateral and normal forces between patterned substrates induced by nematic fluctuations

We consider a nematic liquid crystal confined by two parallel flat substrates whose anchoring conditions vary periodically in one lateral direction. Within the Gaussian approximation, we study the effective forces between the patterned substrates induced by the thermal fluctuations of the nematic director. The shear force oscillates as function of the lateral shift between the patterns on the lower and the upper substrates. We compare the strength of this fluctuation-induced lateral force with the lateral van der Waals force arising from chemically structured adsorbed monolayers. The fluctuation-induced force in normal direction is either repulsive or attractive, depending on the model parameters.Comment: 9 pages, 9 figure

Applying bim to built heritage with complex shapes: The ice house of filarete's ospedale maggiore in milan, Italy

This paper presents the development of a BIM model for a stratified historic structure characterized by a complex geometry: Filarete's Ospedale Maggiore ice house, one of the few remaining historic ice houses in Milan (Fig. 1). Filarete, a well-known Renaissance architect and theorist, planned the hospital in the 15th century, but the ice house was built two centuries later with a double-storey irregular octagonal brick structure, half under and half above ground, that enclosed another circular structure called the ice room. The purpose of the double-walled structure was to store ice in the middle and store and preserve perishable food and medicine at the outer side of the ice room. During World War II, major portions of the hospital and the above-ground section of the ice house was bombed and heavily damaged. Later, in 1962, the hospital was restored and rehabilitated into a university, with the plan to conceal the ice house's remaining structure in the courtyard, which ultimately was excavated and incorporated into a new library for the university. A team of engineers, architects, and students from Politecnico di Milano and Carleton University conducted two heritage recording surveys in 2015 and 2016 to fully document the existing condition of the ice house, resulting in an inclusive laser scanner and photogrammetric point cloud dataset. The point cloud data was consolidated and imported into two leading parametric modelling software, Autodesk Revit© and Graphisoft ArchiCAD©, with the goal to develop two BIMs in parallel in order to study and compare the software BIM workflow, parametric capabilities, attributes to capture the complex geometry with high accuracy, and the duration for parametric modelling. The comparison study of the two software revealed their workflow limitations, leading to integration of the BIM generative process with other pure modelling software such as Rhinoceros©. The integrative BIM process led to the production of a comprehensive BIM model that documented related historic data and the existing physical state of the ice house, to be used as a baseline for preventive maintenance, monitoring, and future conservation projects

Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model.

BackgroundThe aneurysm clip impact-compression model of spinal cord injury (SCI) is a standard injury model in animals that closely mimics the primary mechanism of most human injuries: acute impact and persisting compression. Its histo-pathological and behavioural outcomes are extensively similar to human SCI. To understand the distinct molecular events underlying this injury model we analyzed global mRNA abundance changes during the acute, subacute and chronic stages of a moderate to severe injury to the rat spinal cord.ResultsTime-series expression analyses resulted in clustering of the majority of deregulated transcripts into eight statistically significant expression profiles. Systematic application of Gene Ontology (GO) enrichment pathway analysis allowed inference of biological processes participating in SCI pathology. Temporal analysis identified events specific to and common between acute, subacute and chronic time-points. Processes common to all phases of injury include blood coagulation, cellular extravasation, leukocyte cell-cell adhesion, the integrin-mediated signaling pathway, cytokine production and secretion, neutrophil chemotaxis, phagocytosis, response to hypoxia and reactive oxygen species, angiogenesis, apoptosis, inflammatory processes and ossification. Importantly, various elements of adaptive and induced innate immune responses span, not only the acute and subacute phases, but also persist throughout the chronic phase of SCI. Induced innate responses, such as Toll-like receptor signaling, are more active during the acute phase but persist throughout the chronic phase. However, adaptive immune response processes such as B and T cell activation, proliferation, and migration, T cell differentiation, B and T cell receptor-mediated signaling, and B cell- and immunoglobulin-mediated immune response become more significant during the chronic phase.ConclusionsThis analysis showed that, surprisingly, the diverse series of molecular events that occur in the acute and subacute stages persist into the chronic stage of SCI. The strong agreement between our results and previous findings suggest that our analytical approach will be useful in revealing other biological processes and genes contributing to SCI pathology