mAb806 binding to epidermal growth factor receptor: a computational study by Ng, Yao Zong, Kannan, Srinivasaraghavan, Lane, David P., Fuentes, Gloria, Verma, Chandra Shekhar

“…To explore this interaction, we combined molecular docking, steered molecular dynamics, and equilibrium molecular dynamics simulations. Our computational models reveal that the antibody induces local unfolding around the epitope to form the antibody–EGFR complex. …”
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Modelling frequency-based neural responses to deep brain stimulation in Parkinson’s disease by Sermon, JJ

“…To investigate observed signal changes from DBS, we analyse and develop computational models of signals whose frequency signature changes in response to neuromodulation. …”

Mechanisms that promote the evolution of cross-reactive antibodies upon vaccination with designed influenza immunogens by Yang, Leerang, Caradonna, Timothy M, Schmidt, Aaron G, Chakraborty, Arup K

“…Here, we develop a computational model to interrogate antibody evolution by affinity maturation after immunization with two types of immunogens: a heterotrimeric "chimera" hemagglutinin that is enriched for the RBS epitope relative to other B cell epitopes and a cocktail composed of three non-epitope-enriched homotrimers of the monomers that comprise the chimera. …”
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Cerebellar-driven cortical dynamics can enable task acquisition, switching and consolidation by Pemberton, J, Chadderton, P, Costa, RP

“…We introduce a computational model of cerebellar networks that learn to drive cortical networks with task-outcome predictions. …”

Azimuthal solar synchronization and aerodynamic neuro-optimization: an empirical study on slime-mold-inspired neural networks for solar UAV range optimization by Graheeth, Hazare, Mohamed Thariq, Hameed Sultan, Dariusz, Mika, Farah Syazwani, Shahar, Grzegorz, Skorulski, Marek, Nowakowski, Andriy, Holovatyy, Ile, Mircheski, Wojciech, Giernacki

“…Our approach integrates a computational model of slime mold networks with a simulation environment to optimize both the solar energy collection and the aerodynamic performance of UAVs. …”
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Conformational ensemble modeling of multi-domain proteins with experimental data by Zhu, Guanhua

“…We have implemented our computational model and ensemble optimization to two systems of multi-domain proteins on the coarse-grained and atomistic levels respectively. …”
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N-methyl-D-aspartate receptor- antibody encephalitis impairs maintenance of attention to items in working memory by Dor, A, Harrison, C, Irani, SR, Al-Diwani, A, Grogan, J, Manohar, S

“…NMDA receptors (NMDAR) may be crucial to working memory (WM). Computational models predict that they sustain neural firing and produce associative memory, which may underpin maintaining and binding information respectively. …”

Characterizing Image Recognition Difficulty in Artificial and Biological Visual Processing by Cummings, Jesse E.

“…In recent years, computational models trained to do object recognition have become increasingly capable. …”
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Antigen presentation dynamics shape the antibody response to variants like SARS-CoV-2 Omicron after multiple vaccinations with the original strain by Yang, Leerang, Van Beek, Matthew, Wang, Zijun, Muecksch, Frauke, Canis, Marie, Hatziioannou, Theodora, Bieniasz, Paul D, Nussenzweig, Michel C, Chakraborty, Arup K

“…We reveal mechanisms underlying this observation by combining computational modeling with data from vaccinated humans. After the first dose, limited antigen availability in germinal centers (GCs) results in a response dominated by B cells that target immunodominant epitopes that are mutated in an Omicron-like variant. …”
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A saliency detection model using low-level features based on wavelet transform by İmamoğlu, Nevrez, Lin, Weisi, Fang, Yuming

“…Then, we propose a computational model for the saliency map from these features. …”
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Multiple-level feature-based measure for retargeted image quality by Zhang, Yabin, Lin, Weisi, Li, Qiaohong, Cheng, Wentao, Zhang, Xinfeng

“…Objective image retargeting quality assessment aims to use computational models to predict the retargeted image quality consistent with subjective perception. …”
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Sig2GRN : a software tool linking signaling pathway with gene regulatory network for dynamic simulation by Zhang, Fan, Liu, Runsheng, Zheng, Jie

“…Background: Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. …”
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Semantic object processing is modulated by prior scene context by Krugliak, A, Draschkow, D, Võ, ML-H, Clarke, A

“…Yet, the time course and mechanisms of how contextual information supports access to semantic object information is unclear. We used computational modelling and EEG to test how context influences semantic object processing. …”

Exploring the regulation of myofilament function in the heart using experimental and computational approaches by Folkmanaite, M

“…The goal of this thesis is to address this knowledge gap.</p> <p>Computational modelling and experimental techniques were used to investigate the regulation of myofilament function. …”

Rapid Simulation of Electro-Chemo-Mechanical Deformation of Li-ion Batteries Based On Porous Electrode Theory by Ipers, Gerrit, Jiao, Junning, Pathak, Shakul, Fang, Ruqing, Berliner, Marc D, Li, Wei, Li, Weihan, Braatz, Richard D, Bazant, Martin Z, Zhu, Juner

“…Here, we implemented the coupled model into the open-source software PETLION for millisecond-scale simulation. The computational model is parameterized using values gathered from literature, tested under varying conditions, briefly compared to real-world observations, and qualitatively analyzed to find parameter-output relations.…”
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Interfacial fracture behavior of double-ceramic-layer thermal barrier coating system with segmented structure by Li, Biao, Fan, Xueling, Wang, Tiejun, Zhou, Kun

“…The contact between interface crack faces was taken into account in the computational model. The effects of segmentation pattern, geometrical and material properties of the top coats on the delamination behavior were discussed. …”
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A hybrid of ant colony optimization, genetic algorithm and flux balance analysis for optimization of succinic acid production in Escherichia coli by Tan, Jun Bin, Choon, Yee Wen, Moorthy, Kohbalan, Hasyiya Karimah, Adli, Muhammad Akmal, Remli, Mohd Arfian, Ismail, Zuwairie, Ibrahim, Mohd Saberi, Mohamad

“…Researchers build computational models of E. coli to analyze and modify their metabolic network. …”
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MAAD: A Model and Dataset for "Attended Awareness" in Driving by Gopinath, Deepak, Rosman, Guy, Stent, Simon, Terahata, Katsuya, Fletcher, Luke, Argall, Brenna, Leonard, John

“…We propose a computational model to estimate a person's attended awareness of their environment. …”
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Modelling the rheology of living cell cytoplasm: poroviscoelasticity and fluid-to-solid transition by Thekkethil, Namshad, Köry, Jakub, Guo, Ming, Stewart, Peter S., Hill, Nicholas A., Luo, Xiaoyu

“…To gain insights into this complex rheological behaviour, we construct a computational model for the cell cytoplasm as a poroviscoelastic material formulated on the principles of nonlinear continuum mechanics, where we model the cytoplasm as a porous viscoelastic scaffold with an embedded viscous fluid flowing between the pores to model the cytosol. …”
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Identification of potential critical virulent sites based on hemagglutinin of influenza A virus in past pandemic strains by Yin, Rui, Fransiskus, Xaverius Ivan, Zheng, Jie, Zhou, Xinrui, Chow, Vincent T. K., Kwoh, Chee Keong

“…With increasingly huge biological data, computational modeling is a good technique for analyzing data, providing novel insight into significant patterns and rules. …”
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