24 papers · ranked by Valyu relevance
Poonam Vishwakarma, Akhila Melarkode Vattekatte, Nicolas Shinada, Julien Diharce + 7 more
'Julien Diharce' 'Carla Martins' 'Frédéric Cadet' 'Fabrice Gardebien' 'Catherine Etchebest' 'Aravindan Arun Nadaradjane' 'Alexandre G. de Brevern' 'Honoo Satake'] VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared…
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…
Jason Chen, Ayisha Zia, Fengbin Wang, Jie Hou + 2 more
Understanding the structures of proteins has numerous applications, such as vaccine development. It is a slow and labor-intensive task to manually build protein structures from experimental electron density maps, therefore, machine learning approaches have been proposed to automate this process. However, most of the…
Sophie Libkind, Andrew Baas, Micah Halter, Evan Patterson + 1 more
'James P. Fairbanks'] Pandemic management requires that scientists rapidly formulate and analyse epidemiological models in order to forecast the spread of disease and the effects of mitigation strategies. Scientists must modify existing models and create novel ones in light of new biological data and policy changes…
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…
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…
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…
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…
Asher Moldwin, Amarda Shehu
Multimodal neural networks integrating protein language models (PLMs) with structure-derived features are increasingly common for predicting mutation effects, yet fundamental mechanisms remain poorly characterized. In this paper, we articulate and address two key questions: (i) do these architectures exploit…
Mathias Peirlinck, Kevin Linka, Juan A. Hurtado, Gerhard A. Holzapfel + 1 more
Personalized computational simulations have emerged as a vital tool to understand the biomechanical factors of a disease, predict disease progression, and design personalized intervention. Material modeling is critical for realistic biomedical simulations, and poor model selection can have life-threatening consequences…
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…
Mateusz Bieniek, Ben Cree, Rachael Pirie, Joshua Horton + 2 more
Automated free energy calculations for the prediction of binding free energies of congeneric series of ligands to a protein target are growing in popularity, but building reliable initial binding poses for the ligands is challenging. Here, we introduce the open-source FEgrow workflow for building userdefined congeneric…
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…
Bruna Silva, Marco Domingos, Sandra Amado, Juliana R. Dias + 4 more
'Paula Pascoal-Faria' 'Ana C. Maurício' 'Nuno Alves' 'Dimitrios Kouroupis'] Understanding the complex mechanical behavior of osteochondral tissues in silico is essential for improving experimental models and advancing research in joint health and degeneration. This review provides a comprehensive analysis of the…
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…
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…
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…
Adelinde M. Uhrmacher, Peter I. Frazier, Reiner Hähnle, Franziska Klügl + 8 more
'Franziska Klügl' 'Fabian Lorig' 'Bertram Ludäscher' 'Laura Nenzi' 'Cristina Ruiz-Martín' 'Bernhard Rumpe⋆' 'Claudia Szabo' 'Gabriel Wainer' 'Pia Wilsdorf'] Simulation has become, in many application areas, a sine-qua-non. Most recently, COVID-19 has underlined the importance of simulation studies and limitations in…
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…