Computation, Volume 5, Issue 4 (December 2017) – 8 articles

The routinely made assumptions for simulating solid materials are briefly summarized, since they need to be critically assessed when new aspects become important, such as excited states, finite temperature, time-dependence, etc. The significantly higher computer power combined with improved experimental data open new areas for interdisciplinary research, for which new ideas and concepts are needed. Full article

Heterogeneous clusters are a widely utilized class of supercomputers assembled from different types of computing devices, for instance CPUs and GPUs, providing a huge computational potential. Programming them in a scalable way exploiting the maximal performance introduces numerous challenges such as optimizations for different computing devices, dealing with multiple levels of parallelism, the application of different programming models, work distribution, and hiding of communication with computation. We utilize the lattice Boltzmann method for fluid flow as a representative of a scientific computing application and develop a holistic implementation for large-scale CPU/GPU heterogeneous clusters. We review and combine a set of best practices and techniques ranging from optimizations for the particular computing devices to the orchestration of tens of thousands of CPU cores and thousands of GPUs. Eventually, we come up with an implementation using all the available computational resources for the lattice Boltzmann method operators. Our approach shows excellent scalability behavior making it future-proof for heterogeneous clusters of the upcoming architectures on the exaFLOPS scale. Parallel efficiencies of more than $90\%$ are achieved leading to $2604.72$ GLUPS utilizing 24,576 CPU cores and 2048 GPUs of the CPU/GPU heterogeneous cluster Piz Daint and computing more than $6.8\times {10}^9$ lattice cells. Full article

By reversing paradigms that normally utilize mathematical models as the basis for nonlinear adaptive controllers, this article describes using the controller to serve as a novel computational approach for mathematical system identification. System identification usually begins with the dynamics, and then seeks to parameterize the mathematical model in an optimization relationship that produces estimates of the parameters that minimize a designated cost function. The proposed methodology uses a DC motor with a minimum-phase mathematical model controlled by a self-tuning regulator without model pole cancelation. The normal system identification process is briefly articulated by parameterizing the system for least squares estimation that includes an allowance for exponential forgetting to deal with time-varying plants. Next, towards the proposed approach, the Diophantine equation is derived for an indirect self-tuner where feedforward and feedback controls are both parameterized in terms of the motor’s math model. As the controller seeks to nullify tracking errors, the assumed plant parameters are adapted and quickly converge on the correct parameters of the motor’s math model. Next, a more challenging non-minimum phase system is investigated, and the earlier implemented technique is modified utilizing a direct self-tuner with an increased pole excess. The nominal method experiences control chattering (an undesirable characteristic that could potentially damage the motor during testing), while the increased pole excess eliminates the control chattering, yet maintains effective mathematical system identification. This novel approach permits algorithms normally used for control to instead be used effectively for mathematical system identification. Full article

Extracorporeal organ perfusion, in which organs are preserved in an isolated, ex vivo environment over an extended time-span, is a concept that has led to the development of numerous alternative preservation protocols designed to better maintain organ viability prior to transplantation. These protocols offer researchers a novel opportunity to obtain extensive sampling of isolated organs, free from systemic influences. Data-driven computational modeling is a primary means of integrating the extensive and multivariate data obtained in this fashion. In this review, we focus on the application of dynamic data-driven computational modeling to liver pathophysiology and transplantation based on data obtained from ex vivo organ perfusion. Full article

This paper is devoted to modelling tissue growth with a deformable cell model. Each cell represents a polygon with particles located at its vertices. Stretching, bending and pressure forces act on particles and determine their displacement. Pressure-dependent cell proliferation is considered. Various patterns of growing tissue are observed. An application of the model to tissue regeneration is illustrated. Approximate analytical models of tissue growth are developed. Full article

We present a hierarchical coarse-graining framework for modeling semidilute polymer solutions, based on the wavelet-accelerated Monte Carlo (WAMC) method. This framework forms a hierarchy of resolutions to model polymers at length scales that cannot be reached via atomistic or even standard coarse-grained simulations. Previously, it was applied to simulations examining the structure of individual polymer chains in solution using up to four levels of coarse-graining (Ismail et al., J. Chem. Phys., 2005, 122, 234901 and Ismail et al., J. Chem. Phys., 2005, 122, 234902), recovering the correct scaling behavior in the coarse-grained representation. In the present work, we extend this method to the study of polymer solutions, deriving the bonded and non-bonded potentials between coarse-grained superatoms from the single chain statistics. A universal scaling function is obtained, which does not require recalculation of the potentials as the scale of the system is changed. To model semi-dilute polymer solutions, we assume the intermolecular potential between the coarse-grained beads to be equal to the non-bonded potential, which is a reasonable approximation in the case of semidilute systems. Thus, a minimal input of microscopic data is required for simulating the systems at the mesoscopic scale. We show that coarse-grained polymer solutions can reproduce results obtained from the more detailed atomistic system without a significant loss of accuracy. Full article

A self-organizing map (SOM) is an artificial neural network algorithm that can learn from the training data consisting of objects expressed as vectors and perform non-hierarchical clustering to represent input vectors into discretized clusters, with vectors assigned to the same cluster sharing similar numeric or alphanumeric features. SOM has been used widely in transcriptomics to identify co-expressed genes as candidates for co-regulated genes. I envision SOM to have great potential in characterizing heterogeneous sequence motifs, and aim to illustrate this potential by a parallel presentation of SOM with a set of numerical vectors and a set of equal-length sequence motifs. While there are numerous biological applications of SOM involving numerical vectors, few studies have used SOM for heterogeneous sequence motif characterization. This paper is intended to encourage (1) researchers to study SOM in this new domain and (2) computer programmers to develop user-friendly motif-characterization SOM tools for biologists. Full article

We propose a limited-memory quasi-Newton method using the bad Broyden update and apply it to the nonlinear equations that must be solved to determine the effective Fermi momentum in the weighted density approximation for the exchange energy density functional. This algorithm has advantages for nonlinear systems of equations with diagonally dominant Jacobians, because it is easy to generalize the method to allow for periodic updates of the diagonal of the Jacobian. Systematic tests of the method for atoms show that one can determine the effective Fermi momentum at thousands of points in less than fifteen iterations. Full article