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

Docosahexaenoic acid regulates the formation of lipid rafts: A unified view from experiment and simulation

(2018) Stephen R. Wassall et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of 13C NMR Relaxation Times and Their Distributions

(2018) Pan Chen et al.   BIOMACROMOLECULES

Mechanism and structure studies of cinnamaldehyde/cyclodextrins inclusions by computer simulation and NMR technology

(2018) Qiaomei Sun et al.   CARBOHYDRATE POLYMERS

A molecular dynamics simulation study on the conformational stability of amylose-linoleic acid complex in water

(2018) Lilin Cheng et al.   CARBOHYDRATE POLYMERS

Molecular dynamics simulations and applications in computational toxicology and nanotoxicology

(2018) Chandrabose Selvaraj et al.   FOOD AND CHEMICAL TOXICOLOGY

Silibinin is a direct inhibitor of STAT3

(2018) Sara Verdura et al.   FOOD AND CHEMICAL TOXICOLOGY

Molecular dynamics simulations of zinc oxide solubility: From bulk down to nanoparticles

(2018) Laura Escorihuela et al.   FOOD AND CHEMICAL TOXICOLOGY

Functionality of ovalbumin during Chinese steamed bread-making processing

(2018) Shangyuan Sang et al.   FOOD CHEMISTRY

Structural and antigenic properties of thermally treated gluten proteins

(2018) Nicoleta Stănciuc et al.   FOOD CHEMISTRY

The cryoprotectant effect of xylooligosaccharides on denaturation of peeled shrimp ( Litopenaeus vannamei ) protein during frozen storage

(2018) Bin Zhang et al.   FOOD HYDROCOLLOIDS

Molecular simulation of the water-triolein-oleic acid mixture: Local structure and thermodynamic properties

(2018) E. Couallier et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-grained molecular dynamics study of membrane distillation through meso-size graphene channels

(2018) Hui Zhang et al.   JOURNAL OF MEMBRANE SCIENCE

Soybean oil-based nanoemulsion systems in absence and presence of curcumin: Molecular dynamics simulation approach

(2018) Fariba Moghaddasi et al.   JOURNAL OF MOLECULAR LIQUIDS

Crystal structures and molecular dynamics studies of the inclusion compounds of β -citronellol in β -cyclodextrin, heptakis(2,6-di- O -methyl)- β -cyclodextrin and heptakis(2,3,6-tri- O -methyl)- β -cyclodextrin

(2018) Katerina Fourtaka et al.   JOURNAL OF MOLECULAR STRUCTURE

Computer-Aided Formulation Design for a Highly Soluble Lutein–Cyclodextrin Multiple-Component Delivery System

(2018) Qianqian Zhao et al.   MOLECULAR PHARMACEUTICS

Understanding the interactions between sebum triglycerides and water: a molecular dynamics simulation study

(2018) Anna Sofia Tascini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields

(2018) Hwankyu Lee   PLoS One

Gas-phase complexation of α-/β-cyclodextrin with amino acids studied by ion mobility-mass spectrometry and molecular dynamics simulations

(2018) Yinjuan Chen et al.   TALANTA

Microbial Starch-Converting Enzymes: Recent Insights and Perspectives

(2018) Ming Miao et al.   COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY

Cryoprotective roles of trehalose and alginate oligosaccharides during frozen storage of peeled shrimp ( Litopenaeus vannamei )

(2017) Bin Zhang et al.   FOOD CHEMISTRY

Effects of high hydrostatic pressure on lipase from Rhizopus chinensis : I. Conformational changes

(2017) Gang Chen et al.   Innovative Food Science & Emerging Technologies

Elucidation of pressure-induced lid movement and catalysis behavior of Rhizopus chinensis lipase

(2017) Gang Chen et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Insights into Cryoprotective Roles of Carrageenan Oligosaccharides in Peeled Whiteleg Shrimp (Litopenaeus vannamei) during Frozen Storage

(2017) Bin Zhang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Effects of High Pressure on Phospholipid Bilayers

(2017) Wei Ding et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of physicochemical properties of peptides from soy protein on their antimicrobial activity

(2017) Ning Xiang et al.   PEPTIDES

Pressure effects on collective density fluctuations in water and protein solutions

(2017) Daniela Russo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

(2017) Charles R. Watts et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Thermal stability of the complex formed between carotenoids from sea buckthorn ( Hippophae rhamnoides L.) and bovine β-lactoglobulin

(2017) Iuliana Aprodu et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

A study of the effect of amino acids on pasting and short-term retrogradation properties of rice starch based on molecular dynamics simulation

(2017) Jie Wan et al.   STARCH-STARKE

Molecular dynamics simulation of the interaction between dense-phase carbon dioxide and the myosin heavy chain

(2017) Shucheng Liu et al.   Journal of CO2 Utilization

Solution Structure and Constrained Molecular Dynamics Study of Vitamin B12Conjugates of the Anorectic Peptide PYY(3-36)

(2016) Kelly E. Henry et al.   ChemMedChem

A molecular perspective on the limits of life: Enzymes under pressure

(2016) Huang et al.   Condensed Matter Physics

More than a look into a crystal ball: protein structure elucidation guided by molecular dynamics simulations

(2016) Marcel Bermudez et al.   DRUG DISCOVERY TODAY

Effect of flavonols on wine astringency and their interaction with human saliva

(2016) Raúl Ferrer-Gallego et al.   FOOD CHEMISTRY

Effects of thermal and electric fields on soybean trypsin inhibitor protein: A molecular modelling study

(2016) Brinda Harish Vagadia et al.   Innovative Food Science & Emerging Technologies

Energetic and conformational features linked to the monomeric and dimeric states of bovine BLG

(2016) Martiniano Bello et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Methodology for identification of pore forming antimicrobial peptides from soy protein subunits β-conglycinin and glycinin

(2016) Ning Xiang et al.   PEPTIDES

Pressure-induced conformational switch of an interfacial protein

(2016) Quentin R. Johnson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking and molecular dynamics simulations of the ternary complex nisin 2 :lipid II

(2016) Sam Mulholland et al.   Scientific Reports

Enantioselective developmental toxicity and immunotoxicity of pyraclofos toward zebrafish (Danio rerio)

(2015) Shulin Zhuang et al.   AQUATIC TOXICOLOGY

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

(2015) Giuseppina Raffaini et al.   Beilstein Journal of Organic Chemistry

Predict the glass transition temperature and plasticization of β-cyclodextrin/water binary system by molecular dynamics simulation

(2015) Guohui Zhou et al.   CARBOHYDRATE RESEARCH

Isoflurane does not aggregate inside POPC bilayers at high pressure: Implications for pressure reversal of general anaesthesia

(2015) J.R. Wieteska et al.   CHEMICAL PHYSICS LETTERS

Nisin as a Food Preservative: Part 1: Physicochemical Properties, Antimicrobial Activity, and Main Uses

(2015) Adem Gharsallaoui et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Interaction mechanism between green tea extract and human α-amylase for reducing starch digestion

(2015) Ming Miao et al.   FOOD CHEMISTRY

Isolation and characterisation of sericin antifreeze peptides and molecular dynamics modelling of their ice-binding interaction

(2015) Jinhong Wu et al.   FOOD CHEMISTRY

Sugar stereochemistry effects on water structure and on protein stability: The templating concept

(2015) Ravit Edelman et al.   FOOD HYDROCOLLOIDS

Application of molecular dynamics simulation in food carbohydrate research—a review

(2015) Tao Feng et al.   Innovative Food Science & Emerging Technologies

Effect of thermal and electric field treatment on the conformation of Ara h 6 peanut protein allergen

(2015) Sai Kranthi Vanga et al.   Innovative Food Science & Emerging Technologies

Effect of High Electric Field on Secondary Structure of Wheat Gluten

(2015) Ashutosh Singh et al.   INTERNATIONAL JOURNAL OF FOOD PROPERTIES

Self-Assembled Nanoparticle of Common Food Constituents That Carries a Sparingly Soluble Small Molecule

(2015) Deepak Bhopatkar et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Monitoring the heat-induced structural changes of alkaline phosphatase by molecular modeling, fluorescence spectroscopy and inactivation kinetics investigations

(2015) Loredana Dumitrașcu et al.   JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE

Coarse-grained modelling of triglyceride crystallisation: a molecular insight into tripalmitin tristearin binary mixtures by molecular dynamics simulations

(2015) Antonio Pizzirusso et al.   JOURNAL OF PHYSICS D-APPLIED PHYSICS

A Unique Capsular Polysaccharide Structure from the Psychrophilic Marine Bacterium Colwellia psychrerythraea 34H That Mimics Antifreeze (Glyco)proteins

(2015) Sara Carillo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure

(2015) Michael T. Lerch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modelling of noble anaesthetic gases and high hydrostatic pressure effects in lipid bilayers

(2015) Yevgeny Moskovitz et al.   Soft Matter

Binding site of different tannins on a human salivary proline-rich protein evidenced by dissociative photoionization tandem mass spectrometry

(2015) Francis Canon et al.   TETRAHEDRON

Computational close up on protein-protein interactions: how to unravel the invisible using molecular dynamics simulations?

(2015) Christin Rakers et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Structural dynamics of the cell wall precursor lipid II in the presence and absence of the lantibiotic nisin

(2014) Dennis C. Koch et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Molecular Dynamics Simulations of the Adhesion of a Thin Annealed Film of Oleic Acid onto Crystalline Cellulose

(2014) Mir A. A. R. Quddus et al.   BIOMACROMOLECULES

Exploring binding properties of naringenin with bovine β-lactoglobulin: A fluorescence, molecular docking and molecular dynamics simulation study

(2014) Samira Gholami et al.   BIOPHYSICAL CHEMISTRY

Atomic Insights into Distinct Hormonal Activities of Bisphenol A Analogues toward PPARγ and ERα Receptors

(2014) Shulin Zhuang et al.   CHEMICAL RESEARCH IN TOXICOLOGY

High-Pressure Chemical Biology and Biotechnology

(2014) Jerson L. Silva et al.   CHEMICAL REVIEWS

Influence of Pulsed Electric Field onEscherichia coliandSaccharomyces cerevisiae

(2014) Xiaoyun Tao et al.   INTERNATIONAL JOURNAL OF FOOD PROPERTIES

Exposure of thiol groups in the heat-induced denaturation of β-lactoglobulin

(2014) Rosanne N.W. Zeiler et al.   MOLECULAR SIMULATION

Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations

(2014) Nobuhiko Wakai et al.   PLoS One

Role of cavities and hydration in the pressure unfolding of T4 lysozyme

(2014) N. V. Nucci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New insights into heat induced structural changes of pectin methylesterase on fluorescence spectroscopy and molecular modeling basis

(2014) Oana Viorela Nistor et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates

(2013) W.F. Drew Bennett et al.   CANADIAN JOURNAL OF CHEMISTRY

Molecular simulation of adsorption of hydrophobin HFBI to the air–water, DPPC–water and decane–water interfaces

(2013) Stephen R. Euston   FOOD HYDROCOLLOIDS

Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods

(2013) Lili Gai et al.   JOURNAL OF CHEMICAL PHYSICS

On the Electroporation Thresholds of Lipid Bilayers: Molecular Dynamics Simulation Investigations

(2013) Andraž Polak et al.   JOURNAL OF MEMBRANE BIOLOGY

A combined spectroscopic, molecular docking and molecular dynamic simulation study on the interaction of quercetin with β-casein nanoparticles

(2013) Fahimeh Mehranfar et al.   JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY

Effect of High Exogenous Electric Pulses on Protein Conformation: Myoglobin as a Case Study

(2013) Paolo Marracino et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Simulations of Membrane–Sugar Interactions

(2013) Jon Kapla et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Elucidation of structural difference in theaflavins for modulation of starch digestion

(2013) Ming Miao et al.   Journal of Functional Foods

Modeling complex and multi-component food systems in molecular dynamics simulations on the example of chocolate conching

(2013) Maximilian Greiner et al.   Food & Function

ReaxFF molecular dynamics simulations of non-catalytic pyrolysis of triglyceride at high temperatures

(2013) Zhiqiang Zhang et al.   RSC Advances

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Structure and dynamics of β-lactoglobulin in complex with dodecyl sulfate and laurate: A molecular dynamics study

(2012) Martiniano Bello et al.   BIOPHYSICAL CHEMISTRY

Improved stability and controlled release of ω3/ω6 polyunsaturated fatty acids by spring dextrin encapsulation

(2012) Jin Xu et al.   CARBOHYDRATE POLYMERS

Amylose folding under the influence of lipids

(2012) Cesar A. López et al.   CARBOHYDRATE RESEARCH

A multiscale approach to triglycerides simulations: from atomistic to coarse-grained models and back

(2012) Antonio Brasiello et al.   FARADAY DISCUSSIONS

Molecular dynamics simulation of the effect of heat on the conformation of bovine β-lactoglobulin A: A comparison of conventional and accelerated methods

(2012) S.R. Euston   FOOD HYDROCOLLOIDS

Fluorescence spectroscopy and molecular modeling investigations on the thermally induced structural changes of bovine β-lactoglobulin

(2012) Nicoleta Stănciuc et al.   Innovative Food Science & Emerging Technologies

Temperature- and Pressure-Dependent Densities, Self-Diffusion Coefficients, and Phase Behavior of Monoacid Saturated Triacylglycerides: Toward Molecular-Level Insights into Processing

(2012) Maximilian Greiner et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Anticoagulant Activity of a Unique Sulfated Pyranosic (1→3)-β-l-Arabinan through Direct Interaction with Thrombin

(2012) Paula V. Fernández et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms

(2012) Johannes Kirchmair et al.   Journal of Chemical Information and Modeling

Water–water and water–macromolecule interactions in food dehydration and the effects of the pore structures of food on the energetics of the interactions

(2012) J.-C. Wang et al.   JOURNAL OF FOOD ENGINEERING

The Interaction of Polyphenol Flavonoids with β-lactoglobulin: Molecular Docking and Molecular Dynamics Simulation Studies

(2012) Mehdi Sahihi et al.   Journal of Macromolecular Science Part B-Physics

Molecular Dynamics Simulations of Lipid Membrane Electroporation

(2012) Lucie Delemotte et al.   JOURNAL OF MEMBRANE BIOLOGY

The open lid conformation of the lipase is explored in the compressed gas: New insights from molecular dynamic simulation

(2012) Mohammad Reza Housaindokht et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

The Colloidal State of Tannins Impacts the Nature of Their Interaction with Proteins: The Case of Salivary Proline-Rich Protein/Procyanidins Binding

(2012) Olivier Cala et al.   LANGMUIR

Molecular Simulation of Hydrophobin Adsorption at an Oil–Water Interface

(2012) David L. Cheung   LANGMUIR

Cavities determine the pressure unfolding of proteins

(2012) J. Roche et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The initial stage of high-pressure induced β-lactoglobulin aggregation: the long-run simulation

(2011) Gennadiy Reznikov et al.   INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY

Activity and stability enhancement of α-amylase treated with sub- and supercritical carbon dioxide

(2011) Deniz Senyay-Oncel et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling

(2011) Olgun Guvench et al.   Journal of Chemical Theory and Computation

Prediction of Solubility Parameters and Miscibility of Pharmaceutical Compounds by Molecular Dynamics Simulations

(2011) Jasmine Gupta et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Amylose–Vanillin Complexation Assessed by a Joint Experimental and Theoretical Analysis

(2011) Silvio D. Rodríguez et al.   Journal of Physical Chemistry C

Structural behavior of Candida antarctica lipase B in water and supercritical carbon dioxide: A molecular dynamic simulation study

(2011) Mohammad Reza Housaindokht et al.   JOURNAL OF SUPERCRITICAL FLUIDS

Antifreeze glycoprotein agents: structural requirements for activity

(2011) Patricio A Carvajal-Rondanelli et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucanendo-transglycosylase

(2011) Pekka Mark et al.   MOLECULAR SIMULATION

Development of a coarse-grained model for simulations of tridecanoin liquid–solid phase transitions

(2011) Antonio Brasiello et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Carbohydrate force fields

(2011) B. Lachele Foley et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Protein dynamics and enzyme catalysis: Insights from simulations

(2010) John D. McGeagh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

The Behavior of the Hydrophobic Effect under Pressure and Protein Denaturation

(2010) J. Raúl Grigera et al.   BIOPHYSICAL JOURNAL

Modeling the solid-liquid phase transition in saturated triglycerides

(2010) David A. Pink et al.   JOURNAL OF CHEMICAL PHYSICS

Box–Behnken design for studying inclusion complexes of triglycerides and α-cyclodextrin: application to the heating protocol in molecular-dynamics simulations

(2010) Eduardo Walneide C. Almeida et al.   JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY

Investigation of the Inclusions of Puerarin and Daidzin with β-Cyclodextrin by Molecular Dynamics Simulation

(2010) Haiyang Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Pre-Nucleation Structuring of TAG Melts Revealed by Fluorescence Polarization Spectroscopy and Molecular Mechanics Simulations

(2010) E. Dibildox-Alvarado et al.   JOURNAL OF THE AMERICAN OIL CHEMISTS SOCIETY

Electroporation of Cell Membranes: The Fundamental Effects of Pulsed Electric Fields in Food Processing

(2010) Gintautas Saulis   Food Engineering Reviews

Molecular dynamics simulations of a cyclic-DP-240 amylose fragment in a periodic cell: Glass transition temperature and water diffusion

(2009) Frank A. Momany et al.   CARBOHYDRATE POLYMERS

Ice Morphology: Fundamentals and Technological Applications in Foods

(2009) Guillermo Petzold et al.   Food Biophysics

Molecular Binding of Catechins to Biomembranes: Relationship to Biological Activity

(2009) Timothy W. Sirk et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Temperature-Dependent Mechanisms for the Dynamics of Protein-Hydration Waters: A Molecular Dynamics Simulation Study

(2009) M. Vogel   JOURNAL OF PHYSICAL CHEMISTRY B

Experimental Study on Conformational Changes of Lysozyme in Solution Induced by Pulsed Electric Field and Thermal Stresses

(2009) Wei Zhao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Temperature-induced unfolding pathway of a type III antifreeze protein: Insight from molecular dynamics simulation

(2008) Sangeeta Kundu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Modeling of the Triglyceride-Rich Core in Lipoprotein Particles

(2008) Anette Hall et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dual Function of the Hydration Layer around an Antifreeze Protein Revealed by Atomistic Molecular Dynamics Simulations

(2008) David R. Nutt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Food structure and functionality: a soft matter perspective

(2008) Job Ubbink et al.   Soft Matter