Related papers: Parallel Algorithm for Calculation of the Exact Pa…
The specific heat is a central property of condensed matter systems including polymers and oligomers in their condensed phases. Yet, predictions of this quantity from molecular simulations and successful comparisons to experimental data are…
Lattice models are valuable tools to gain insight into the statistical physics of heteropolymers. We rigorously map the partition function of these models into a vacuum expectation value of a $\mathbb{Z}_2$ lattice gauge theory (LGT), with…
The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several…
We describe a parallel solver for the discretized weakly singular space-time boundary integral equation of the spatially two-dimensional heat equation. The global space-time nature of the system matrices leads to improved parallel…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
Many tasks in data mining and related fields can be formalized as matching between objects in two heterogeneous domains, including collaborative filtering, link prediction, image tagging, and web search. Machine learning techniques,…
We discuss in detail a recently proposed hybrid particle-continuum scheme for complex fluids and evaluate it at the example of a confined homopolymer solution in slit geometry. The hybrid scheme treats polymer chains near the impenetrable…
Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic…
Resolving numerically Vlasov-Poisson equations for initially cold systems can be reduced to following the evolution of a three-dimensional sheet evolving in six-dimensional phase-space. We describe a public parallel numerical algorithm…
The behavior of a Lattice Monte Carlo algorithm (if it is designed correctly) must approach that of the continuum system that it is designed to simulate as the time step and the mesh step tend to zero. However, we show for an algorithm for…
Bridging algorithms are global Monte Carlo moves which allow for an efficient sampling of single polymer chains. In this manuscript we discuss the adaptation of three bridging algorithms from lattice to continuum models, and give details on…
We present a massively parallel algorithm for calculating the self-energy in self-consistent finite temperature perturbation theory for lattice models. The algorithm uses analytic functions with appropriate asymptotic high frequency…
We study the correlators of irregular vertex operators in two-dimensional conformal field theory (CFT) in order to propose an exact analytic formula for calculating numbers of partitions, that is: 1) for given $N,k$, finding the total…
The pivot algorithm is the most efficient known method for sampling polymer configurations for self-avoiding walks and related models. Here we introduce two recent improvements to an efficient binary tree implementation of the pivot…
The LC method described in this work seeks to approximate the roots of polynomial equations in one variable. This book allows you to explore the LC method, which uses geometric structures of Lines L and Circumferences C in the plane of…
As multicore systems continue to gain ground in the High Performance Computing world, linear algebra algorithms have to be reformulated or new algorithms have to be developed in order to take advantage of the architectural features on these…
The calculation of physical quantities by lattice QCD simulations requires in some important cases the determination of the inverse of a very large matrix. In this article we describe how stochastic estimator methods can be applied to this…
The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…
Calculating the correlation in a sliding window is a common method of statistical evaluation of the interconnect between two sets of data. And although the calculation of a single correlation coefficient is not resource-intensive and…
In this work we illustrate our novel quantitative simulation approach for dense amorphous polymer systems, as discussed in our previous work[Kulkarni et al., A Novel Approach for Lattice Simulations of Polymer Chains in Dense Amorphous…