Artificial intelligence in food science and nutrition: a narrative review.

In the late 2010s, artificial intelligence (AI) technologies became complementary to the research areas of food science and nutrition. This review aims to summarize these technological advances by systematically describing the following: the use of AI in other fields (eg, engineering, pharmacy, and medicine); the history of AI in relation to food science and nutrition; the AI technologies currently used in the agricultural and food industries; and some of the important applications of AI in areas such as immunity-boosting foods, dietary assessment, gut microbiome profile analysis, and toxicity prediction of food ingredients. These applications are likely to be in great demand in the near future. This review can provide a starting point for brainstorming and for generating new AI applications in food science and nutrition that have yet to be imagined.

Interaction grand potential between calcium-silicate-hydrate nanoparticles at the molecular level.

Calcium-silicate-hydrate (or C-S-H), an inosilicate, is the major binding phase in cement pastes and concretes and a porous hydrated material made up of a percolated and dense network of crystalline nanoparticles of a mean apparent spherical diameter of ∼5 nm that are each stacks of multiple C-S-H layers. Interaction forces between these nanoparticles are at the origin of C-S-H chemical, physical, and mechanical properties at the meso- and macroscales. These particle interactions and the resulting properties may be affected significantly by nanoparticle density and environmental conditions such as the temperature, relative humidity, or concentration of chemical species in the bulk solution. In this study, we combined grand canonical Monte Carlo simulations and an extension of the mean force integration method to derive the pair potentials. This approach enables realistic simulation of the physical environment surrounding the C-S-H particles. We thus constructed the pair potentials for C-S-H nanoparticles of defined chemical stoichiometry at 10% relative humidity (RH), varying the relative crystallographic orientations at a constant particle density of ρpart ∼ 2.21 mmol L(-1). We found that cohesion between nanoparticles is affected strongly by both the aspect ratio and the crystallographic misorientation of interacting particles. This method and the findings underscore the importance of accounting for relative dimensions and orientation among C-S-H nanoparticles in descriptions of physical and simulated multiparticle aggregates or mesoscale systems.

Theoretical investigation of the interactions in binding pocket of Reverse Transcriptase.

Interactions in proteins have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. In this work we adopt an approach to study these interactions accounting for as many as possible explicit solvent molecules and without the need of a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, and which combined with the MD paradigm results in an ultra accelerated QCMD method for protein-ligand interaction evaluations. We have applied our newly developed method to the Nevirapine (NVP)-Reverse Transcriptase (RT) system. We show how the proposed method leads us to new findings. The advanced QCMD was applied to a system of RT with NVP and it has led to the knowledge of specific groups and atoms that interact with surrounding amino acids of RT and help in drug binding. The information derived from this calculation may be used in designing drugs for NVP resistant virus strains that have binding capability like NVP.

A computational chemistry study on friction of h-MoS2. Part II. Friction anisotropy.

In this work, the friction anisotropy of hexagonal MoS(2) (a well-known lamellar compound) was theoretically investigated. A molecular dynamics method was adopted to study the dynamical friction of two-layered MoS(2) sheets at atomistic level. Rotational disorder was depicted by rotating one layer and was changed from 0° to 60°, in 5° intervals. The superimposed structures with misfit angle of 0° and 60° are commensurate, and others are incommensurate. Friction dynamics was simulated by applying an external pressure and a sliding speed to the model. During friction simulation, the incommensurate structures showed extremely low friction due to cancellation of the atomic force in the sliding direction, leading to smooth motion. On the other hand, in commensurate situations, all the atoms in the sliding part were overcoming the atoms in counterpart at the same time while the atomic forces were acted in the same direction, leading to 100 times larger friction than incommensurate situation. Thus, lubrication by MoS(2) strongly depended on its interlayer contacts in the atomic scale. According to part I of this paper [Onodera, T., et al. J. Phys. Chem. B 2009, 113, 16526-16536], interlayer sliding was source of friction reduction by MoS(2) and was originally derived by its material property (interlayer Coulombic interaction). In addition to this interlayer sliding, the rotational disorder was also important to achieve low friction state.

The effect of R249S carcinogenic and H168R-R249S suppressor mutations on p53-DNA interaction, a multi scale computational study.

In this study we have undertaken the theoretical analysis of the effect of R249S carcinogenic and H168R-R249S suppressor mutation at core domain of the tumor suppressor protein p53, on its natural interaction with DNA using a newly developed method. The results show that the carcinogenic mutation R249S affects the flexibility of L3 loop region in p53, inducing the loss of important hydrogen bonds observed at interaction in the wild-type with DNA, on the other hand the suppressor mutation H168R on the R249S assists in maintaining the wild-type like flexibility of the L3 region in p53 and thus recover the interaction terms lost in the carcinogenic mutation alone. The present study sets a new direction in the development of new drugs that may restore the interactions that lost as a consequence of the carcinogenic mutations in p53.

Quantum chemistry study on absorption spectra, electronic and electrical properties of organic dye on anatase(001).

As the most reactive surface, the stoichiometric O-bridge terminated anatase(001) surface attracted considerable attentions in many application fields. The interfacial electron transfer in dye-sensitized anatase(001) plays a principal role in a variety of photoinduced reactions. In the present work, the UV-vis absorption spectrum of TiO2 bulk and different surface models were calculated by means of tight-binding quantum chemical molecular dynamics program "Colors-excite" for the first time. The thickness dependence on electronic and electrical properties of anatase(001) surface was achieved. The anatase(001) surface with a thickness of 1.0 nm shows excellent electronic and electrical properties. Moreover, the most suitable binding mode (dissociative adsorption) and absorption spectra of perylene with acrylic acid (PAA) on the optimum anatase(001) were investigated. A significant red-shift was observed from the UV-vis absorption spectrum of PAA/anatase(001) system. The red-shift occurring when PAA adsorbed on anatase(001) surface suggests that PAA/anatase(001) may be potential candidate for dye-sensitized solar cell. This study also proposed an effective computational tool "Colors-excite" to study of the electronic excitation properties for both molecular and periodic systems.

Tribochemical reaction dynamics of molybdenum dithiocarbamate on nascent iron surface: a hybrid quantum chemical/classical molecular dynamics study.

Using a hybrid quantum chemical/classical molecular dynamics method, we have studied the tribochemical reaction dynamics of molybdenum dithiocarbamate (MoDTC), a commonly used friction modifier in automobile engine oils. MoDTC molecule adsorbed on rubbing nascent iron surface was situated. We firstly investigated the dynamic behavior of MoDTC molecule on the rubbing Fe(001) surface. During the friction simulation, the elongation of Mo-O bonds was observed, forming the Mo2S4 and thiocarbamic acid molecules. To unveil the detailed mechanism of this bond elongation, the electronic states of the MoDTC molecule and Fe(001) surface were computed, and the catalytic effects of Fe(001) surface to the molecule was found. We also found that extreme friction would influence the complete Mo-O bond dissociation. By using the hybrid quantum chemical/classical molecular dynamics method, we successfully simulated the tribochemical reaction dynamics of MoDTC as a friction modifier and obtained the influences of nascent iron surface and friction on its chemical reaction.

A computational chemistry study on friction of h-MoS(2). Part I. Mechanism of single sheet lubrication.

In this work, we theoretically investigated the friction mechanism of hexagonal MoS(2) (a well-known lamellar compound) using a computational chemistry method. First, we determined several parameters for molecular dynamics simulations via accurate quantum chemistry calculations and MoS(2) and MoS(2-x)O(x) structures were successfully reproduced. We also show that the simulated Raman spectrum and peak shift on X-ray diffraction patterns were in good agreement with those of experiment. The atomic interactions between MoS(2) sheets were studied by using a hybrid quantum chemical/classical molecular dynamics method. We found that the predominant interaction between two sulfur layers in different MoS(2) sheets was Coulombic repulsion, which directly affects the MoS(2) lubrication. MoS(2) sheets adsorbed on a nascent iron substrate reduced friction further due to much larger Coulombic repulsive interactions. Friction for the oxygen-containing MoS(2) sheets was influenced by not only the Coulomb repulsive interaction but also the atomic-scale roughness of the MoS(2)/MoS(2) sliding interface.

A graph theoretical approach for assessing bio-macromolecular complex structural stability.

Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.

Quantum chemical studies for oxidation of morpholine by Cytochrome P450.

Since morpholine oxidation has recently been shown to involve Cytochrome P450, the study on its mechanism at molecular level using quantum chemical calculations for the model of cytochrome active site is reported here. The reaction pathway is investigated for two electronic states, the doublet and the quartet, by means of density functional theory. The results show that morpholine hydroxylation occurs through hydrogen atom abstraction and rebound mechanism. However, in the low spin state, the reaction is concerted and hydrogen atom abstraction yields directly ferric-hydroxy morpholine complex without a distinct rebound step while in quartet state the reaction is stepwise. The presence of nitrogen in a morpholine heterocycle is postulated to greatly facilitate hydrogen abstraction. The hydroxylated product undergoes intramolecular hydrogen atom transfer from hydroxy group to nitrogen, leading to the cleavage of the C-N bond and the formation of 2-(2-aminoethoxy) acetaldehyde. The cleavage of the C-N bond is indicated as the rate-determining step for the studied reaction. The assistance of explicit water molecule is shown to lower the energy barrier for the C-N bond cleavage in enzymatic environment whereas solvent effects mimicked by COSMO solvent model have minor influence on relative energies along the pathway.

Robotic path planning and protein complex modeling considering low frequency intra-molecular loop and domain motions.

A novel algorithm is introduced to deal with intra-molecular motions of loops and domains that undergo proteins at interaction with other proteins. The methodology is based on complex energy landscape sampling and robotic motion planning. Mapping high flexibility regions on the protein underlies the proposed algorithm. This is the first time this type of research has been reported. Application of the methodology to several protein complexes where remarkable backbone rearrangement is observed shows that the new algorithm is able to deal with the problem of change of backbone conformation at protein interaction. We have implemented the module within the system MIAX (Macromolecular interaction assessment computer system) and together with our already reported soft and flexible docking algorithms we have developed a powerful tool for protein function analysis as part of wide genome function evaluation.