Modelling and computer simulation of food structures

Euston, Stephen R.; Costello, G.; Naser, M. A.; Nicolosai, M. L.

doi:10.1533/9781845693671.2.334

Cited by 3 publications

(2 citation statements)

References 127 publications

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“…Nowadays, the rapid increase in computational power and resources has enabled MD simulations to mimic biological systems consisting of over 10000 atoms for several microseconds (Cala et al., ; Couallier et al., ), such as biochemical processes (Dror, Dirks, Grossman, Xu, & Shaw, ; Mark et al, ) and protein–protein interactions (Rakers, Bermudez, Keller, Mortier, & Wolber, ). In addition, new simulation methods have been proposed, such as coarse‐grained (CG) MD simulation (Marrink, de Vries, & Mark, ; Molinero & Goddard, ; Zhang, Liu et al., ), steered MD simulation (Isralewitz, Baudry, Gullingsrud, Kosztin, & Schulten, ; Isralewitz, Gao, & Schulten, ), and accelerated (AC) MD simulations that include essential dynamics, replica exchange MD simulation, hyperdynamics, metadynamics, and temperature‐accelerated dynamics (Euston, ; Watts et al., ). Replica exchange MD simulation is a method used to accelerate sampling rates in MD simulation by performing a number of parallel replica simulations at various temperatures and allowing systems with similar potential energies to sample conformations at different temperatures.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

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Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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“…Consequently, detailed conformational information on individual adsorbed proteins at the tertiary structure level is lacking, with much of the available data confined to studies of the overall properties of a composite layer obtained using indirect methods. One method that may be useful in studying adsorbed protein conformation is computer simulation. , We have recently used a molecular dynamics (MD) simulation to probe the structural changes that occur in nonspecific barley lipid transfer protein (LTP) when it adsorbs to either a water−vacuum interface or a decane−water interface. , Using a conventional MD simulation, we found that LTP adsorbed to both the water−vacuum and decane−water interfaces within the restricted time scale achieved, between 20 and 40 ns. The LTP molecule adsorbed to the water−vacuum interface but did not penetrate into the vacuum-space and did not undergo a significant conformational change from its native state .…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation of Protein Adsorption at Fluid Interfaces: A Comparison of All-Atom and Coarse-Grained Models

Euston

2010

Biomacromolecules

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The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.

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Shear-induced aggregation or disaggregation in edible oils: Models, computer simulation, and USAXS measurements

Townsend

Peyronel

Callaghan-Patrachar

et al. 2017

Journal of Applied Physics

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The effects of shear upon the aggregation of solid objects formed from solid triacylglycerols (TAGs) immersed in liquid TAG oils were modeled using Dissipative Particle Dynamics (DPD) and the predictions compared to experimental data using Ultra-Small Angle X-ray Scattering (USAXS). The solid components were represented by spheres interacting via attractive van der Waals forces and short range repulsive forces. A velocity was applied to the liquid particles nearest to the boundary, and Lees-Edwards boundary conditions were used to transmit this motion to non-boundary layers via dissipative interactions. The shear was created through the dissipative forces acting between liquid particles. Translational diffusion was simulated, and the Stokes-Einstein equation was used to relate DPD length and time scales to SI units for comparison with USAXS results. The SI values depended on how large the spherical particles were (250 nm vs. 25 nm). Aggregation was studied by (a) computing the Structure Function and (b) quantifying the number of pairs of solid spheres formed. Solid aggregation was found to be enhanced by low shear rates. As the shear rate was increased, a transition shear region was manifested in which aggregation was inhibited and shear banding was observed. Aggregation was inhibited, and eventually eliminated, by further increases in the shear rate. The magnitude of the transition region shear, γ̇t, depended on the size of the solid particles, which was confirmed experimentally.

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Modelling and computer simulation of food structures

Cited by 3 publications

References 127 publications

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Molecular Dynamics Simulation of Protein Adsorption at Fluid Interfaces: A Comparison of All-Atom and Coarse-Grained Models

Shear-induced aggregation or disaggregation in edible oils: Models, computer simulation, and USAXS measurements

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