ARTICLE | doi:10.20944/preprints201811.0250.v1
Subject: Physical Sciences, Mathematical Physics Keywords: High-Throughput Molecular Dynamics (HTMD) simulations; Nosé-Hoover Chain (NHC); Canonical ensemble; Graphics Processing Units (GPUs).
Online: 9 November 2018 (15:26:49 CET)
Molecular dynamics simulation is currently the theoretical technique eligible to simulate a wide range of systems from soft condensed matter to biological systems. However, of the excellent results that the technique has arrogated, this approach remains computationally expensive, but with the emergence of the new supercomputing technologies bases on graphics processing units graphical processing units-based systems GPUs, the perspective has changed. The GPUs allow performing large and complex simulations at a significantly reduced time. In this work, we present recent innovations in the acceleration of molecular dynamics in GPUs to simulate non-Hamiltonian systems. In particular, we show the performance of measure-preserving geometric integrator in the canonical ensemble, that is, at constant temperature. We provide a validation and performance evaluation of the code by calculating the thermodynamic properties of a Lennard-Jones fluid. Our results are in excellent agreement with reported data reported from literature, which were calculated with CPUs. The scope and limitations for performing simulations of high-throughput MD under rigorous statistical thermodynamics in the canonical ensemble are discussed and analyzed.
ARTICLE | doi:10.3390/sci2010006
Online: 28 February 2020 (00:00:00 CET)
Ukiyo-e is a traditional Japanese painting style most commonly printed using wood blocks. Ukiyo-e prints feature distinct line work, bright colours, and a non-perspective projection. Most previous research on ukiyo-e styled computer graphics has been focused on creation of 2D images. In this paper we propose a framework for rendering interactive 3D scenes with ukiyo-e style. The rendering techniques use standard 3D models as input and require minimal additional information to automatically render scenes in a ukiyo-e style. The described techniques are evaluated based on their ability to emulate ukiyo-e prints, performance, and temporal coherence.
Subject: Life Sciences, Biochemistry Keywords: molecular graphics; protein visualization; software tools; virtual reality
Online: 12 January 2020 (16:26:54 CET)
Molecular visualisation is fundamental in the current scientific literature, textbooks and dissemination materials, forming an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Visual exploration has become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. Here we first describe a few Swiss Army knives geared towards protein visualisation for everyday use with an existing large user base, then focus on more specialised tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.
ARTICLE | doi:10.20944/preprints202206.0423.v1
Subject: Mathematics & Computer Science, Geometry & Topology Keywords: solid geometry; helix; Chasles’ theorem; platonic helix; tetrahelix; linear algebrea; computer graphics
Online: 30 June 2022 (08:56:22 CEST)
Eric Lord has observed: “In nature, helical structures arise when identical structural subunits combine sequentially, the orientational and translational relation between each unit and its predecessor remaining constant.” This paper proves Lord’s Observation. Constant-time algorithms are given for the segmented helix generated from the intrinsic properties of a stacked object and its conjoining rule. Standard results from screw theory and previous work are combined with corollaries of Lord’s observation to allow calculations of segmented helices from either transformation matrices or four known consecutive points. The construction of these from the intrinsic properties of the rule for conjoining repeated subunits of arbitrary shape is provided, allowing the complete parameters describing the unique segmented helix generated by arbitrary stackings to be easily calculated. Free-libre open-source interactive software and a website is provided which performs this computation for arbitrary prisms along with interactive 3D visualization . We prove that any subunit can produce a toroid-like helix or a maximally-extended helix, forming a continuous spectrum based on joint-face normal twist. This software, website and paper, taken together, compute, render, and catalog an exhaustive “zoo” of 28 uniquely-shaped platonic helices, such as the Boerdijk-Coxeter tetrahelix and various species of helices formed from dodecahedra.
ARTICLE | doi:10.20944/preprints202111.0154.v1
Subject: Engineering, Civil Engineering Keywords: Computer Vision; Synthetic Data; Physics-based Graphics Models; Deep Learning; Post-earthquake Inspections
Online: 8 November 2021 (15:06:45 CET)
Manual visual inspections typically conducted after an earthquake are high-risk, subjective, and time-consuming. Delays from inspections often exacerbate the social and economic impact of the disaster on affected communities. Rapid and autonomous inspection using images acquired from unmanned aerial vehicles offer the potential to reduce such delays. Indeed, a vast amount of re-search has been conducted toward developing automated vision-based methods to assess the health of infrastructure at the component and structure level. Most proposed methods typically rely on images of the damaged structure, but seldom consider how the images were acquired. To achieve autonomous inspections, methods must be evaluated in a comprehensive end-to-end manner, incorporating both data acquisition and data processing. In this paper, we leverage recent advances in computer generated imagery (CGI) to construct a 3D synthetic environment for simulation of post-earthquake inspections that allows for comprehensive evaluation and valida-tion of autonomous inspection strategies. A critical issue is how to simulate and subsequently render the damage in the structure after an earthquake. To this end, a high-fidelity nonlinear finite element model is incorporated in the synthetic environment to provide a representation of earthquake-induced damage; this finite element model, combined with photo-realistic rendering of the damage, is termed herein a physics-based graphics models (PBGM). The 3D synthetic en-vironment with PBGMs provide a comprehensive end-to-end approach for development and validation of autonomous post-earthquake strategies using UAVs, including: (i) simulation of path planning of virtual UAVs and image capture under different environmental conditions; (ii) au-tomatic labeling of captured images, potentially providing an infinite amount of data for training deep neural networks; (iii) availability of the ground truth damage state from the results of the finite-element simulation; and (iv) direct comparison of different approaches to autonomous as-sessments. Moreover, the synthetic data generated has the potential to be used to augment field datasets. To demonstrate the efficacy of PBGMs, models of reinforced concrete moment-frame buildings with masonry infill walls are examined. The 3D synthetic environment employing PBGMs is shown to provide an effective testbed for development and validation of autonomous vision-based post-earthquake inspections that can serve as an important building block for ad-vancing autonomous data to decision frameworks.
ARTICLE | doi:10.20944/preprints201706.0114.v1
Subject: Life Sciences, Biochemistry Keywords: proteins；time-varying； parallel； architectures；Conditional Random Fields (CRF)；Graphics Processing Units； Block Coordinate Descent algorithm
Online: 26 June 2017 (05:47:40 CEST)
Proteins are the workhorses of the cell that perform biological functions by interacting with other proteins. Many statistical methods for protein-protein interaction (PPI) have been studied without considering time-dependent changes in networks and the functionalities. I introduced a novel method that models PPI networks as being dynamic in nature and evolving time-varying multivariate distribution with Conditional Random Fields (CRF). This research is directed towards implementing this new combinatorial algorithm on massively parallel architectures such as Graphics Processing Units (GPUs) for efficient computations for large scale bioinformatics datasets. I compared Conditional Random Fields (CRF) and the proposed novel method using CRF combined with the Block Coordinate Descent algorithm for human protein-protein interaction data set. Both are implemented on GPU-Accelerated Computing Architecture and the proposed novel method showed the advantages in predicting protein-protein interaction sites. I also show that the proposed approach is more efficient in 6.13% than standalone CRF++ in predicting protein-protein interaction sites.
CASE REPORT | doi:10.20944/preprints202006.0053.v1
Subject: Mathematics & Computer Science, Numerical Analysis & Optimization Keywords: Algebraic iterative reconstruction; ART methods; Row-action methods; Graphics Cards; Tomographic imaging; Medical imaging; Seismic Imaging; Walnut Imaging.
Online: 5 June 2020 (14:27:06 CEST)
In this article we present a SCILAB implementation of algebraic iterative reconstruction methods for discretisation of inverse problems in imaging. These so-called row action methods rely on semi-convergence for achieving the necessary regularisation of the problem. We implement this method using SCILAB and provide a few simplified test problems: medical tomography, seismic tomography and walnut tomography.Numerical results show the capability of this method for the original and perturbed right-hand side vector.