scholarly journals Thermodynamics, dynamics, and structure of supercritical water at extreme conditions

2020 ◽  
Vol 22 (28) ◽  
pp. 16051-16062 ◽  
Author(s):  
Tae Jun Yoon ◽  
Lara A. Patel ◽  
Taeho Ju ◽  
Matthew J. Vigil ◽  
Alp T. Findikoglu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Supercritical Water ◽  
Structural Changes ◽  
Md Simulations ◽  
Extreme Conditions ◽  
Melting Line

Molecular dynamics (MD) simulations to understand the thermodynamic, dynamic, and structural changes in supercritical water across the Frenkel line and the melting line have been performed.

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

scholarly journals Mechanistic picture for chemo-mechanical couplings in a bacterial proton-coupled oligopeptide transporter from Streptococcus thermophilus

2020 ◽  
Author(s):  
Kalyan Immadisetty ◽  
Mahmoud Moradi
Keyword(s):  
Molecular Dynamics ◽  
Cell Membrane ◽  
Proton Transport ◽  
Structural Changes ◽  
Streptococcus Thermophilus ◽  
Md Simulations ◽  
Electrochemical Gradient ◽  
Binding Region ◽  
Conformational Switch ◽  
Sequence Identity

AbstractProton-coupled oligopeptide transporters (POTs) use the proton electrochemical gradient to transport peptides across the cell membrane. Despite the significant biological and biomedical relevance of these proteins, a detailed mechanistic picture for chemo-mechanical couplings involved in substrate/proton transport and protein structural changes is missing. We therefore performed microsecond-level molecular dynamics (MD) simulations of bacterial POT transporter PepTSt, which shares ~80% sequence identity with the human POT, PepT1, in the substrate binding region. Three different conformational states of PepTSt were simulated including, (i) occluded, apo, (ii) inward-facing, apo, and (iii) inward-facingoccluded, Leu-Ala bound. We propose that the interaction of R33 with E299 and E300 acts as a conformational switch (i.e., to trigger the conformational change from an inward-to outward-facing state) in the substrate transport. Additionally, E299 and E400 should disengage from interacting with the substrate either through protonation or through co-ordination with a cation for the substrate to get transported.

scholarly journals An Overview of Molecular Dynamics Simulation for Food Products and Processes

Processes ◽  
2022 ◽  
Vol 10 (1) ◽  
pp. 119
Author(s):  
Andrea Smith ◽  
Xin Dong ◽  
Vijaya Raghavan
Keyword(s):  
Molecular Dynamics ◽  
Food Processing ◽  
Structural Changes ◽  
Food Product ◽  
Food Products ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Chicken Breast ◽  
Optimal Processing ◽  
History Of

Molecular dynamics (MD) simulation is a particularly useful technique in food processing. Normally, food processing techniques can be optimized to favor the creation of higher-quality, safer, more functional, and more nutritionally valuable food products. Modeling food processes through the application of MD simulations, namely, the Groningen Machine for Chemical Simulations (GROMACS) software package, is helpful in achieving a better understanding of the structural changes occurring at the molecular level to the biomolecules present in food products during processing. MD simulations can be applied to define the optimal processing conditions required for a given food product to achieve a desired function or state. This review presents the development history of MD simulations, provides an in-depth explanation of the concept and mechanisms employed through the running of a GROMACS simulation, and outlines certain recent applications of GROMACS MD simulations in the food industry for the modeling of proteins in food products, including peanuts, hazelnuts, cow’s milk, soybeans, egg whites, PSE chicken breast, and kiwifruit.

scholarly journals Deswelling of microfibril bundles in drying wood studied by small-angle neutron scattering and molecular dynamics

Cellulose ◽  
2021 ◽  
Author(s):  
Aleksi Zitting ◽  
Antti Paajanen ◽  
Lauri Rautkari ◽  
Paavo A. Penttilä
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Structural Changes ◽  
Md Simulations ◽  
Cellulose Microfibrils ◽  
Dynamic Vapor Sorption ◽  
Time Resolved ◽  
Constant Rate

Abstract Structural changes of cellulose microfibrils and microfibril bundles in unmodified spruce cell wall due to drying in air were investigated using time-resolved small-angle neutron scattering (SANS). The scattering analysis was supported with dynamic vapor sorption (DVS) measurements to quantify the macroscopic drying kinetics. Molecular dynamics (MD) simulations were carried out to aid in understanding the molecular-level wood-water interactions during drying. Both SANS experiments and simulations support the notion that individual cellulose microfibrils remain relatively unaffected by drying. There is, however, a significant decrease in fibril-to-fibril distances in microfibril bundles. Both scattering and DVS experiments showed two distinct drying regions: constant-rate drying and falling-rate drying. This was also supported by the MD simulation results. The shrinking of the fibril bundles starts at the boundary of these two regions, which is accompanied by a strong decrease in the diffusivity of water in between the microfibrils. Graphic abstract

scholarly journals Molecular Dynamics Simulations of Dislocations in TlBr Crystals under an Electrical Field

MRS Advances ◽  
2016 ◽  
Vol 1 (35) ◽  
pp. 2459-2464 ◽  
Author(s):  
X. W. Zhou ◽  
M. E. Foster ◽  
P. Yang ◽  
F. P. Doty
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Vacancy Concentration ◽  
Radiation Detection ◽  
Md Simulations ◽  
Electrical Field ◽  
Electrical Fields ◽  
Charge Model ◽  
Aging Mechanisms ◽  
Dynamics Simulations

ABSTRACTTlBr crystals have superior radiation detection properties; however, their properties degrade in the range of hours to weeks when an operating electrical field is applied. To account for this rapid degradation using the widely-accepted vacancy migration mechanism, the vacancy concentration must be orders of magnitude higher than any conventional estimates. The present work has incorporated a new analytical variable charge model in molecular dynamics (MD) simulations to examine the structural changes of materials under electrical fields. Our simulations indicate that dislocations in TlBr move under electrical fields. This discovery can lead to new understanding of TlBr aging mechanisms under external fields.

scholarly journals Observing spontaneous, accelerated substrate binding in molecular dynamics simulations of glutamate transporters

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250635
Author(s):  
Jiali Wang ◽  
Peifan Li ◽  
Xiaozhen Yu ◽  
Christof Grewer
Keyword(s):  
Molecular Dynamics ◽  
Bound States ◽  
Structural Changes ◽  
Excitatory Amino Acid ◽  
Substrate Binding ◽  
Glutamate Transporter ◽  
Md Simulations ◽  
Glutamate Transporters ◽  
Side Chain ◽  
Excitatory Amino Acid Transporter

Glutamate transporters are essential for removing the neurotransmitter glutamate from the synaptic cleft. Glutamate transport across the membrane is associated with elevator-like structural changes of the transport domain. These structural changes require initial binding of the organic substrate to the transporter. Studying the binding pathway of ligands to their protein binding sites using molecular dynamics (MD) simulations requires micro-second level simulation times. Here, we used three methods to accelerate aspartate binding to the glutamate transporter homologue Gltph and to investigate the binding pathway. 1) Two methods using user-defined forces to prevent the substrate from diffusing too far from the binding site. 2) Conventional MD simulations using very high substrate concentrations in the 0.1 M range. The final, substrate bound states from these methods are comparable to the binding pose observed in crystallographic studies, although they show more flexibility in the side chain carboxylate function. We also captured an intermediate on the binding pathway, where conserved residues D390 and D394 stabilize the aspartate molecule. Finally, we investigated glutamate binding to the mammalian glutamate transporter, excitatory amino acid transporter 1 (EAAT1), for which a crystal structure is known, but not in the glutamate-bound state. Overall, the results obtained in this study reveal new insights into the pathway of substrate binding to glutamate transporters, highlighting intermediates on the binding pathway and flexible conformational states of the side chain, which most likely become locked in once the hairpin loop 2 closes to occlude the substrate.

Molecular Dynamics Simulation of the Alpha-Recoil Nucleus Displacement Cascade in Zirconolite

2001 ◽  
Author(s):  
L. Veiller ◽  
JP. Crocombette ◽  
C. Meis ◽  
D. Ghaleb
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Md Simulations ◽  
Recoil Nucleus ◽  
Dynamics Simulation ◽  
Α Decay ◽  
Cell Parameters ◽  
Displacement Cascades ◽  
Pair Potentials ◽  
High Level

Abstract Zirconolite (CaZrTi2O7) has been proposed as a crystalline ceramic host for the long-term disposal of actinides extracted from high-level nuclear waste (e.g. France) and from excess weapons-grade plutonium (e.g. USA). The disintegration of radionuclides induces modifications of the crystalline structure. During α-decay of actinides, localized cascades of displaced atoms occur primarily because of ballistic collisions in the material from the emitted α-recoil nuclei. Under α-decay irradiation, zirconolite undergoes a crystalline to amorphous transformation, which is associated to a volume expansion. We have focused our study on the understanding of radiation-induced structural changes at the atomic level in this ceramic. Molecular Dynamics (MD) has been used in the simulation of displacement cascades in zirconolite. Original Buckingham pair potentials have been established for zirconolite to characterize the two body short-range interactions between different ionic pairs. We present the potential parameters fitted to the structural equilibrium properties of the crystal. This fitting reproduces the characteristics of the cell parameters of zirconolite within 4% and gives reasonable values for the bulk modulus and the specific heat. The MD method is applied to determine the threshold displacement energies for the various sublattices. Finally, we have modelled the effects of displacement cascades in zirconolite, due to the α-recoil nuclei. For that purpose, two MD simulations of high recoil kinetic energies (2 and 6 keV) were performed. The preliminary results show that the complex matrix zirconolite tends to a structural disordering for high PKA energy values although a partial recrystallization step is observed during the energy dissipation.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

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