26 papers · ranked by Valyu relevance
Daniel Russel, Keren Lasker, Ben Webb, Javier Velázquez-Muriel + 4 more
'Elina Tjioe' 'Dina Schneidman-Duhovny' 'Bret Peterson' 'Andrej Sali'] A set of software tools for building and distributing models of macromolecular assemblies uses an integrative structure modeling approach, which casts the building of models as a computational optimization problem where information is encoded into a…
Zachary K. Stine, James E. Deitrick
The proliferation of methods for modeling of human meaning-making constitutes a powerful class of instruments for the analysis of complex semiotic systems. However, the field lacks a general theoretical framework for describing these modeling practices across various model types in an apples-to-apples way. In this…
Muyuan Chen
Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational…
Kari Gaalswyk, Mir Ishruna Muniyat, Justin L. MacCallum
Biomolecular structure determination has long relied on heuristics based on physical insight; however, recent efforts to model conformational ensembles and to make sense of sparse, ambiguous, and noisy data have revealed the value of detailed, quantitative physical models in structure determination. We review these two…
Authors not listed
Accelerating computational materials science relies not only on hardware advances but also on software that increases the ease of working with the relevant abstractions. Creation and manipulation of crystal structures is a part of many routine materials science workflows. In this work, we demonstrate how fine tuning…
Lim Heo, Collin Arbour, Michael Feig
Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict…
Mihaly Varadi, Sreenath Nair, Ian Sillitoe, Gerardo Tauriello + 28 more
While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated…
Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello + 2 more
The most frequently used approach for protein structure prediction is currently homology modeling. The 3D model building phase of this methodology is critical for obtaining an accurate and biologically useful prediction. The most widely employed tool to perform this task is MODELLER. This program implements the…
Authors not listed
Validating chemical synthesis success requires confirming the desired product using various analytical techniques. While spectroscopic data collection is increasingly automated, interpreting results remains a major bottleneck often requiring expert input. With advances in laboratory automation and high-throughput…
Qiang Zou, Qiqiang Zheng, Zhihong Tang, Shuming Gao
Variational design is a well-recognized CAD technique due to the increased design efficiency. It often presents as a parametric family of solid models. Although effective, this way of working cannot handle design requirements that go beyond parametric changes. Such design requirements are not uncommon today due to the…
Michael Alverson, Sterling Baird, Ryan Murdock, Taylor Sparks
The idea of materials discovery has excited and perplexed research scientists for centuries. Several different methods have been employed to find new types of materials, ranging from the arbitrary replacement of atoms in a crystal structure to advanced machine learning methods for predicting entirely new crystal…
Aidan J. Hughes, Paul Gardner, Keith Worden
The prospect of informed and optimal decision-making regarding the operation and maintenance (O&M) of structures provides impetus to the development of structural health monitoring (SHM) systems. A probabilistic risk-based framework for decision-making has already been proposed. The framework comprises four key…
Tarja Knuuttila, Andrea Loettgers
The omnipresence of the same basic equations, function forms, algorithms, and quantitative methods is one of the most spectacular characteristics of contemporary modeling practice. Recently, the emergence of the discussion of templates and template transfer has addressed this striking cross-disciplinary reach of…
Tomoya Horiguchi, Takahito Tomoto, Tsukasa Hirashima
In science education, conventional problem practice hardly helps students reach “conceptual understanding” with which they can solve various problems by making appropriate models of target systems. Students often superficially read the solution of a problem and apply it wrongly to others without understanding the…
N. Furian, M. O’Sullivan, C. Walker, S. Vössner + 1 more
Conceptual Modeling (CM) is a fundamental step in a simulation project. Nevertheless, it is only recently that structured approaches towards the definition and formulation of conceptual models have gained importance in the Discrete Event Simulation (DES) community. As a consequence, frameworks and guidelines for…
Authors not listed
High-entropy layered double hydroxides (HE-LDHs) have shown great potential in oxygen evolution reaction (OER) catalysis due to their tunable compositions and electronic structures. However, the synergistic effects between multiple vacancies, such as metal and oxygen vacancies, remain poorly understood and challenging…
Kevin Maik Jablonka, Andrew S. Rosen, Aditi S. Krishnapriyan, Berend Smit
The space of all plausible materials for a given application is so large that it cannot be explored using a brute-force approach. This is, in particular, the case for reticular chemistry which provides materials designers with a practically infinite playground on different length scales. One promising approach to guide…
Kelsey D'Souza
—Modeling should play a central role in K-12 STEM education, where it could make classes much more engaging. A model underlies every scientific theory, and models are central to all the STEM disciplines (Science, Technology, Engineering, Math). This paper describes executable concept modeling of STEM concepts using…
Marius-Constantin Ilau, Tristan Caulfield, David Pym
The nature of information security has been, and probably will continue to be, marked by the asymmetric competition of attackers and defenders over the control of an uncertain environment. The reduction of this degree of uncertainty via an increase in understanding of that environment is a primary objective for both…
Vladimir Kondratyev, Marian Dryzhakov, Timur Gimadiev, Dmitriy Slutskiy
In this work, we provide further development of the junction tree variational autoencoder (JT VAE) architecture in terms of implementation and application of the internal feature space of the model. Pretraining of JT VAE on a large dataset and further optimization with a regression model led to a latent space that can…
Mariana Gómez-Schiavon, Hana El-Samad
Mathematical models continue to be essential for deepening our understanding of biology. On one extreme, simple or small-scale models help delineate general biological principles. However, the parsimony of detail in these models as well as their assumption of modularity and insulation make them inaccurate for…
Ester Comellas, Sandra J. Shefelbine
Endochondral ossification, the process by which long bones grow in length, is regulated by mechanical forces. Computational models, specifically finite element models, have been used for decades to understand the role of mechanical loading on endochondral ossification. This perspective outlines the stages of model…
Niloofar Shahidi, Michael Pan, Kenneth Tran, Edmund J. Crampin + 1 more
Hierarchical modelling is essential to achieving complex, large-scale models. However, not all modelling schemes support hierarchical composition, and correctly mapping points of connection between models requires comprehensive knowledge of each model’s components and assumptions. To address these challenges in…
Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
Reproducible, understandable models that can be reused and combined to true multi-scale systems are required to solve the present and future challenges of systems biology. However, many mathematical models are still built for a single purpose and reusing them in a different context can be challenging due to an…
Sabah Al‐Fedaghi
In the systems and software modeling field, a conceptual model involves modeling with concepts to support development and design. An example of a conceptual model is a description developed using the Unified Modeling Language (UML). UML uses a model multiplicity formulation approach, wherein a number of models are used…
Jonathan Karr, Rahuman S. Malik-Sheriff, James Osborne, Gilberto Gonzalez-Parra + 14 more
'Gilberto Gonzalez-Parra' 'Eric Forgoston' 'Ruth Bowness' 'Yaling Liu' 'Robin Thompson' 'Winston Garira' 'Jacob Barhak' 'John Rice' 'Marcella Torres' 'Hana M. Dobrovolny' 'Tingting Tang' 'William Waites' 'James A. Glazier' 'James R. Faeder' 'Alexander Kulesza'] During the COVID-19 pandemic, mathematical modeling of…