scholarly journals Validating the CHARMM36m Protein Force Field with LJ-PME Reveals Altered Hydrogen Bonding Dynamics under Elevated Pressures

2021 ◽  
Author(s):  
You Xu ◽  
Jing Huang
Keyword(s):  
Hydrogen Bonds ◽  
Force Field ◽  
Md Simulations ◽  
Temperature Phase ◽  
Elevated Pressures ◽  
Wide Range ◽  
Thermodynamic Conditions ◽  
Model Protein ◽  
Temperature And Pressure ◽  
Good Agreement

<p>The pressure-temperature phase diagram is important to our understanding of the physics of biomolecules. Compared to studies on temperature effects, studies of the pressure dependence of protein dynamic are rather limited. Molecular dynamics (MD) simulations with fine-tuned force fields (FFs) offer a powerful tool to explore the influence of thermodynamic conditions on proteins. Here we evaluate the transferability of the CHARMM36m (C36m) protein force field at varied pressures compared with NMR data using ubiquitin as a model protein. The pressure dependences of J couplings for hydrogen bonds and order parameters for internal motion are in good agreement with experiment. We demonstrate that the C36m FF combined with the LJ-PME method is suitable for simulations in a wide range of temperature and pressure. As the ubiquitin remains stable up to 2500 bar, we identify the mobility and stability of different hydrogen bonds in response to pressure. Based on those results, C36m is expected to be applied to more proteins in the future to further investigate protein dynamics under elevated pressures.</p>

scholarly journals Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
You Xu ◽  
Jing Huang
Keyword(s):  
Hydrogen Bonds ◽  
Force Field ◽  
Md Simulations ◽  
Temperature Phase ◽  
Particle Mesh Ewald ◽  
Elevated Pressures ◽  
Wide Range ◽  
Thermodynamic Conditions ◽  
Model Protein ◽  
Good Agreement

AbstractThe pressure-temperature phase diagram is important to our understanding of the physics of biomolecules. Compared to studies on temperature effects, studies of the pressure dependence of protein dynamic are rather limited. Molecular dynamics (MD) simulations with fine-tuned force fields (FFs) offer a powerful tool to explore the influence of thermodynamic conditions on proteins. Here we evaluate the transferability of the CHARMM36m (C36m) protein force field at varied pressures compared with NMR data using ubiquitin as a model protein. The pressure dependences of J couplings for hydrogen bonds and order parameters for internal motion are in good agreement with experiment. We demonstrate that the C36m FF combined with the Lennard-Jones particle-mesh Ewald (LJ-PME) method is suitable for simulations in a wide range of temperature and pressure. As the ubiquitin remains stable up to 2500 bar, we identify the mobility and stability of different hydrogen bonds in response to pressure. Based on those results, C36m is expected to be applied to more proteins in the future to further investigate protein dynamics under elevated pressures.

scholarly journals On the Transferability of CHARMM36m Protein Force Field with LJ-PME: Hydrogen Bonding Dynamics under Elevated Pressures

2021 ◽  
Author(s):  
You Xu ◽  
Jing Huang
Keyword(s):  
Phase Diagram ◽  
Force Field ◽  
Temperature Phase ◽  
Elevated Pressures ◽  
Nmr Data ◽  
Wide Range ◽  
Model Protein ◽  
Temperature And Pressure ◽  
Temperature Phase Diagram ◽  
Hydrogen Bonding Dynamics

The pressure-temperature phase diagram is significant to understanding the physics of biomolecules. In this study we evaluated the transferability of CHARMM36m (C36m) protein force field (FF) in varied pressures using ubiquitin as a model protein compared with NMR data. We demonstrate that C36m FF combining with the LJ-PME method is suitable for simulations in a wide range of temperature and pressure.

scholarly journals On the Transferability of CHARMM36m Protein Force Field with LJ-PME: Hydrogen Bonding Dynamics under Elevated Pressures

2021 ◽  
Author(s):  
You Xu ◽  
Jing Huang
Keyword(s):  
Phase Diagram ◽  
Force Field ◽  
Temperature Phase ◽  
Elevated Pressures ◽  
Nmr Data ◽  
Wide Range ◽  
Model Protein ◽  
Temperature And Pressure ◽  
Temperature Phase Diagram ◽  
Hydrogen Bonding Dynamics

The pressure-temperature phase diagram is significant to understanding the physics of biomolecules. In this study we evaluated the transferability of CHARMM36m (C36m) protein force field (FF) in varied pressures using ubiquitin as a model protein compared with NMR data. We demonstrate that C36m FF combining with the LJ-PME method is suitable for simulations in a wide range of temperature and pressure.

scholarly journals A hierarchical Bayesian framework for force field selection in molecular dynamics simulations

2016 ◽  
Vol 374 (2060) ◽  
pp. 20150032 ◽  
Author(s):  
S. Wu ◽  
P. Angelikopoulos ◽  
C. Papadimitriou ◽  
R. Moser ◽  
P. Koumoutsakos
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Force Field ◽  
Computational Cost ◽  
Md Simulations ◽  
Bayesian Framework ◽  
Underlying Structure ◽  
Hierarchical Bayesian ◽  
Wide Range ◽  
Selection Of

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

Assessment of Current Chemiluminescence Kinetics Models at Engine Conditions

2012 ◽  
Vol 134 (5) ◽  
Author(s):  
Eric Petersen ◽  
Madeleine Kopp ◽  
Nicole Donato ◽  
Felix Güthe
Keyword(s):  
Chemical Kinetics ◽  
Cost Effective ◽  
Gas Turbine Combustor ◽  
Kinetics Models ◽  
Elevated Pressures ◽  
Optical Diagnostic ◽  
Wide Range ◽  
Time Histories ◽  
Temperature And Pressure ◽  
A Current

Chemiluminescence continues to be of interest as a cost-effective optical diagnostic for gas turbine combustor health monitoring. However, most chemical kinetics mechanisms of the chemiluminescence of target species such as OH*, CH*, and CO2* were developed from atmospheric-pressure data. The present paper presents a study wherein the ability of current kinetics models to predict the chemiluminescence trends at engine pressures was assessed. Shock-tube experiments were performed in highly diluted mixtures of H2/O2/Ar at a wide range of pressures to evaluate the ability of a current kinetics model to predict the measured trends. At elevated pressures up to 15 atm, the currently used reaction rate of H + O + M = OH* + M (i.e., without any pressure dependence) significantly over predicts the amount of OH* formed. Other important chemiluminescence species include CH* and CO2*, and separate experiments were performed to assess the validity of existing chemical kinetics mechanisms for both of these species at elevated pressures. A pressure excursion using methane-oxygen mixtures highly diluted in argon was performed up to about 15 atm, and the time histories of CH* and CO2* were measured over a range of temperatures from about 1700 to 2300 K. It was found that the existing CH* mechanism captured the T and P trends rather well, but the CO2* mechanism did a poor job of capturing both the temperature and pressure behavior. With respect to the modeling of collider species, it was found that the current OH* model performs well for N2, but some improvements can be made for CO2.

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

scholarly journals Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Mayank Misra ◽  
Thomas JL Mustard ◽  
David J. Giesen ◽  
Teng Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Moisture Content ◽  
Force Field ◽  
Moisture Sorption ◽  
Md Simulations ◽  
A Value ◽  
Moisture Sorption Isotherm ◽  
Molecular Dynamics Methods ◽  
Grand Canonical ◽  
Good Agreement

<p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br></div>

scholarly journals Development and Validation of Fluorinated Amino Acid Parameters for use with the AMBER ff15ipq Protein Force Field

2022 ◽  
Author(s):  
Darian Yang ◽  
Angela Gronenborn ◽  
Lillian Chong
Keyword(s):  
Force Field ◽  
Aromatic Amino Acids ◽  
Md Simulations ◽  
Water Molecules ◽  
Relaxation Rates ◽  
Structure And Dynamics ◽  
Experimental Values ◽  
Development And Validation ◽  
Explicit Water ◽  
Good Agreement

We developed force field parameters for fluorinated aromatic amino acids enabling molecular dynamics (MD) simulations of fluorinated proteins. These parameters are tailored to the AMBER ff15ipq protein force field and enable the modeling of 4, 5, 6, and 7F-tryptophan, 3F- and 3,5F-tyrosine, and 4F- or 4-CF3-phenylalanine. The parameters include 181 unique atomic charges derived using the Implicitly Polarized Charge (IPolQ) scheme in the presence of SPC/Eb explicit water molecules and 9 unique bond, angle, or torsion terms. Our simulations of benchmark peptides and proteins maintain expected conformational propensities on the μs-timescale. In addition, we have developed an open-source Python program to calculate fluorine relaxation rates from MD simulations. The extracted relaxation rates from protein simulations are in good agreement with experimental values determined by 19F NMR. Collectively, our results illustrate the power and robustness of the IPolQ lineage of force fields for modeling structure and dynamics of fluorine containing proteins at the atomic level.

THEORETICAL DESCRIPTION OF METHANE HYDRATE EQUILIBRIUM IN A WIDE RANGE OF TEMPERATURE AND PRESSURE

2012 ◽  
Vol 01 (02) ◽  
pp. 1250017 ◽  
Author(s):  
RAVIL ZHDANOV ◽  
OLEG SUBBOTIN ◽  
LI-JEN CHEN ◽  
VLADIMIR BELOSLUDOV
Keyword(s):  
High Temperatures ◽  
Methane Hydrate ◽  
Cell Structure ◽  
Pure Water ◽  
Theoretical Description ◽  
Guest Molecules ◽  
Wide Range ◽  
Temperature And Pressure ◽  
Stability Area ◽  
Good Agreement

Theoretical approach was developed for description of clathrate hydrates stability area at low and modestly high temperatures on molecular level. The approach permits to account for interactions between guest molecules and dependence of unit cell structure upon guest's sort, temperature and pressure. Non-ideality of the gas phase was accounted using Van-der-Waals equation of state. Within this approach, methane hydrate calculations have been performed both for low temperature and low pressure region (in equilibrium with ice Ih) and for modestly high temperatures and pressures (in equilibrium with liquid pure water). Calculations show the notable dependence of hydrates thermodynamic properties upon the guest-guest interactions. For methane hydrates, the guest-guest interaction energy can reach 10% of the guest-host value. The results of calculations are in good agreement with available experimental data. This method is applicable for accurate prediction of clathrate hydrate stability in a wide range of P–T conditions.

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