scholarly journals Erratum to Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other

2014 ◽  
Vol 10 (4) ◽  
pp. 1834-1834
Author(s):  
Casey T. Andrews ◽  
Adrian H. Elcock
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Acid Solutions ◽  
Amino Acid Solutions ◽  
Dynamics Simulations

scholarly journals New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (89) ◽  
pp. 48621-48631 ◽  
Author(s):  
Eleanor R. Turpin ◽  
Sam Mulholland ◽  
Andrew M. Teale ◽  
Boyan B. Bonev ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amino Acid Residues ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Dynamics Simulations

Ab initio based force field and molecular dynamics simulations of crystalline TATB

2004 ◽  
Vol 120 (15) ◽  
pp. 7059-7066 ◽  
Author(s):  
Richard H. Gee ◽  
Szczepan Roszak ◽  
Krishnan Balasubramanian ◽  
Laurence E. Fried
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

A Reactive Force Field (ReaxFF) for Molecular Dynamics Simulations of NiO Reduction in H2Environments

2017 ◽  
Vol 78 (1) ◽  
pp. 2765-2771
Author(s):  
Simon Oberhoffer ◽  
Albert M Iskandarov ◽  
Yoshitaka Umeno
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Dynamics Simulations

scholarly journals First-Principles-Based Interatomic Potential for SI and Its Thermal Conductivity

2011 ◽  
Author(s):  
Keivan Esfarjani ◽  
Gang Chen ◽  
Asegun Henry
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Thermal Properties ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Density Functional ◽  
Interatomic Potential ◽  
Force Constants ◽  
Dynamics Simulations

Based on first-principles density-functional calculations, we have developed and tested a force-field for silicon, which can be used for molecular dynamics simulations and the calculation of its thermal properties. This force field uses the exact Taylor expansion of the total energy about the equilibrium positions up to 4th order. In this sense, it becomes systematically exact for small enough displacements, and can reproduce the thermodynamic properties of Si with high fidelity. Having the harmonic force constants, one can easily calculate the phonon spectrum of this system. The cubic force constants, on the other hand, will allow us to compute phonon lifetimes and scattering rates. Results on equilibrium Green-Kubo molecular dynamics simulations of thermal conductivity as well as an alternative calculation of the latter based on the relaxation-time approximation will be reported. The accuracy and ease of computation of the lattice thermal conductivity using these methods will be compared. This approach paves the way for the construction of accurate bulk interatomic potentials database, from which lattice dynamics and thermal properties can be calculated and used in larger scale simulation methods such as Monte Carlo.

scholarly journals A Novel Quali-Quantitative Defect of VWF

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1032-1032
Author(s):  
Tom Van De Berg ◽  
Alice Todaro ◽  
Joyce van Beers ◽  
Kanin Wichapong ◽  
Floor Heubel-Moenen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Genetic Analysis ◽  
Molecular Dynamics Simulations ◽  
Mrna Level ◽  
Bleeding Tendency ◽  
Unknown Significance ◽  
Dynamics Simulations ◽  
Von Willebrand

Abstract Background Von Willebrand Factor (VWF) is a multimeric protein largely involved in both primary and secondary hemostasis. The diagnosis and classification of von Willebrand Disease (VWD) patients can be challenging. In this poster we explore the genetic defects and their structural consequences in a VWD patient with a disproportionately high bleeding phenotype for her VWD severity. A 31-year old female, initially diagnosed with VWD type 1, presented herself with a bleeding tendency (ISTH-BAT 13) disproportionate to the severity of her VWD with antigen levels of 36%. Additional analysis showed decreased FVIII-binding at 28%. The combination of both quantitative and functional defects of VWF was an indication for further genetic analysis in order to better define the subtype of VWD. Aims Genetic and structural analysis of VWF in a patient with a disproportionally high bleeding phenotype with regard to a mild decrease in VWF antigen. Methods Routine laboratory analysis for VWD was performed. Genetic screening was performed by exome sequencing of hemostasis related genes. VWF mRNA analysis was carried out by RT-PCR and Sanger sequencing. The X-ray structure of furin in complex with a peptide-based inhibitor (PDB ID: 6YD7) was used as a template to construct furin-VWF (759HR(R760S)SKRS764) complex. The derived structures (furin in complex with WT/R760S-VWF) were subjected to molecular dynamics (MD) simulations (200ns) and binding free energy (BFE) calculations by using standard parameters and protocols implemented in AMBER20 program. Results Routine analysis showed PFA-ADP and PFA EPI >300 seconds, VWF:ACT of 37% with a VWF:AG of 36%. Collagen binding and FVIII-binding were 46% and 28% respectively. Genetic analysis of the VWF gene disclosed 2 heterozygous variants of unknown significance (VUS): c.2771 G>A (exon 21, p.Arg924Gln) has a 1-2.5% population prevalence and has been previously described in type 1 and 2N VWD. The other VUS (c.2278 C>A; exon 17) is a novel mutation predicting a major amino acid substitution (p.Arg760Ser) in the D2-domain of VWF. Sequencing of exons 17 and 21 in the patient's VWF mRNA revealed homozygosity for the mutated allele at both mutation sites, indicating that the two variants are in cis and that the 'normal' allele is not expressed at mRNA level. Molecular dynamics simulations of the novel c.2278 C>A mutation (Arg760Ser) predicts a markedly decreased binding of furin to its VWF binding site, possibly decreasing or preventing VWF pro-peptide cleavage. This in turn has been shown to lead to reduced FVIII-binding of VWF. Conclusion Genetic analysis shows one polymorphism (c.2771 G>A) and one variation of unknown significance (c.2278 C>A) in the patient's VWF-gene. The polymorphism is known to be of low pathogenicity. The c. 2278 C>A mutation was not known in any of the mutation databases and is a novel VWF mutation. Both mutations were shown to be present on the same allele. As the wild-type allele was not expressed on mRNA level, all of the patient's VWF protein includes both amino acid substitutions. Modeling and molecular dynamics simulations show a markedly decreased affinity of furin to its cleavage site on the VWF protein due to the Arg760Ser substitution, likely resulting in a persistent pro-peptide binding to the mature VWF protein. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

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