An Algorithm for Tensor Product Approximation of Three-Dimensional Material Data for Implicit Dynamics Simulations

2018 ◽  
pp. 156-168 ◽  
Author(s):  
Krzysztof Podsiadło ◽  
Marcin Łoś ◽  
Leszek Siwik ◽  
Maciej Woźniak
Keyword(s):  
Tensor Product ◽  
Three Dimensional ◽  
Material Data ◽  
Tensor Product Approximation ◽  
Dynamics Simulations

scholarly journals Online biophysical predictions for SARS-CoV-2 proteins

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luciano Kagami ◽  
Joel Roca-Martínez ◽  
Jose Gavaldá-García ◽  
Pathmanaban Ramasamy ◽  
K. Anton Feenstra ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Static Structure ◽  
Homologous Proteins ◽  
Structure Based Drug Design ◽  
Protein Protein Interaction ◽  
Link Type ◽  
Dynamics Simulations ◽  
Β Sheet

Abstract Background The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. Main We present a website (https://bio2byte.be/sars2/) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, β-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour. Conclusion The https://bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.

scholarly journals Polymer cyclization for the emergence of hierarchical nanostructures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chaojian Chen ◽  
Manjesh Kumar Singh ◽  
Katrin Wunderlich ◽  
Sean Harvey ◽  
Colette J. Whitfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Hierarchical Structures ◽  
Structural Similarity ◽  
Vital Role ◽  
Nanomaterial Synthesis ◽  
Wide Range ◽  
Linear Poly ◽  
Polymer Folding ◽  
Dynamics Simulations

AbstractThe creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here we demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike and higher-ordered structures. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.

Rheology of Two- and Three-dimensional Granular Mixtures Under Uniform Shear Flow: Enskog Kinetic Theory Versus Molecular Dynamics Simulations

2006 ◽  
Vol 8 (2) ◽  
pp. 103-115 ◽  
Author(s):  
José María Montanero ◽  
Vicente Garzó ◽  
Meheboob Alam ◽  
Stefan Luding
Keyword(s):  
Molecular Dynamics ◽  
Shear Flow ◽  
Kinetic Theory ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Uniform Shear ◽  
Uniform Shear Flow ◽  
Granular Mixtures ◽  
Theory Versus ◽  
Dynamics Simulations

Molecular Dynamics Study of Ion Impact Phenomena and Compressive Stress in Thin Films

1993 ◽  
Vol 317 ◽  
Author(s):  
N.A. Marks ◽  
P. Guan ◽  
D.R. Mckenzie ◽  
B.A. PailThorpe
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
Carbon Films ◽  
Loss Mechanism ◽  
Ion Energy ◽  
Lennard Jones ◽  
Impact Phenomena ◽  
Ion Impact ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTMolecular dynamics simulations of nickel and carbon have been used to study the phenomena due to ion impact. The nickel and carbon interactions were described using the Lennard-Jones and Stillinger-Weber potentials respectively. The phenomena occurring after the impact of 100 e V to 1 keV ions were studied in the nickel simulations, which were both two and three-dimensional. Supersonic focussed collision sequences (or focusons) were observed, and associated with these focusons were unexpected sonic bow waves, which were a major energy loss mechanism for the focuson. A number of 2D carbon films were grown and the stress in the films as a function of incident ion energy was Measured. With increasing energy the stress changed from tensile to compressive and reached a maximum around 50 eV, in agreement with experiment.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

scholarly journals Analysis of the effect of bore/stroke ratio and scavenge port angles on the scavenging process in a two-stroke boosted uniflow scavenged direct injection gasoline engine

2017 ◽  
Vol 232 (13) ◽  
pp. 1799-1814 ◽  
Author(s):  
Xinyan Wang ◽  
Jun Ma ◽  
Hua Zhao
Keyword(s):  
Gasoline Engine ◽  
Direct Injection ◽  
Three Dimensional ◽  
Orientation Angle ◽  
Swirl Flow ◽  
Delivery Ratio ◽  
Boost Pressure ◽  
Baseline Design ◽  
Dynamics Simulations ◽  
Scavenging Efficiency

In this study, a two-stroke boosted uniflow scavenged direct injection gasoline (BUSDIG) engine was proposed and researched to achieve aggressive engine downsizing and downspeeding. Compared to loop or cross scavenged two-stroke engines, the BUSDIG engine can achieve excellent scavenging performance and be operated with higher boost pressure as well as the absence of air and fuel short-circuiting. As a fundamental engine geometric parameter, the bore/stroke (B/S) ratio would directly affect the scavenging process in the uniflow scavenged two-stroke engine. Three-dimensional computational fluid dynamics simulations were used to investigate the scavenging process in the BUSDIG engine with different B/S ratios. Four B/S ratios of 0.66, 0.8, 1, and 1.3 were analyzed. The results indicate that a bigger B/S ratio leads to deteriorated swirl flow motion but better delivery ratio, scavenging efficiency, and charging efficiency. In order to fulfil the potential of the BUSDIG engine with different B/S ratios, two key scavenge port angles, i.e. axis inclination angle (AIA) and swirl orientation angle (SOA), were varied from the baseline design (AIA = 90°, SOA = 20°) to study their effects on the scavenging process for each B/S ratio design. Overall, a larger AIA leads to lower swirl ratio (SR) but achieves better scavenge performance, which is crucial for a large B/S ratio design. A small SOA design leads to noticeably lower SR but superior scavenging performances for a small B/S ratio design. An intermediate SOA, e.g. 10 and 20°, is preferred to improve the scavenging for a large B/S ratio design.

scholarly journals Study of Pseudomonas aeruginosa PPF-1 biofilm formation using microfluidics: effect of magnesium on biofilm detachment in engineered conduits

2021 ◽  
Author(s):  
William Y. Harvey ◽  
Cynthia Gagné-Thivierge ◽  
Sepideh Fakari ◽  
Jean Barbeau ◽  
Steve Charette ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Reference Strain ◽  
Mechanical Stability ◽  
Three Dimensional ◽  
Opportunistic Pathogen ◽  
Shear Stresses ◽  
Density Maps ◽  
Biofilm Detachment ◽  
Flow Systems ◽  
Dynamics Simulations

The bacterium Pseudomonas aeruginosa is an opportunistic pathogen in certain organisms, including humans, but can also survive and proliferate in natural and engineered water systems. Microfluidic technology can address hydrodynamic questions related to bacterial contamination of water flow systems and infrastructure. In this work, a microfluidic approach was devised to study the effect of shear stresses on biofilms from a dental unit waterline (DUWL)-isolated P. aeruginosa strain, PPF-1. During application of relevant shear stress levels to DUWLs, the response of the PPF-1 biofilm was observed and compared to a clinical P. aeruginosa reference strain, PAO1. The response measurements were repeated for biofilms exposed to additional Mg2+ ions. Using a microfluidic approach to transforming optical density maps into three-dimensional images, we applied computational fluid dynamics simulations and determined the critical shear stresses for biofilm sloughing. In the absence of Mg2+, PPF-1 biofilms showed weaker attachment than PAO1 biofilms, resulting in continuous slough/regrowth cycles triggered by applied shear stresses of 1.42 +/- 0.32 Pa. Introducing Mg2+ into the PPF-1 biofilm culture medium seemed to place the biofilm into a viscoplastic mechanical state, thereby increasing mechanical stability, which resulted in elevated tolerances to shear stresses up to a critical value of 5.43 +/- 1.52 Pa. This resulted in a propensity for less frequent but more catastrophic sloughing events like that observed for the PAO1 reference strain. This suggests that in a low ionic environment, biofilms from the PPF-1 strain can result in higher and more continuous ejection of biofilm materials, possibly leading to increased downstream colonization of engineered flow systems.

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