We develop a many-body force field (FF) for tantalum based on extensive ab initio quantum mechanical (QM) calculations and illustrate its application with molecular dynamics (MD). As input data to the FF we use ab initio methods (LAPW-GGA) to calculate: (i) the zero temperature equation of state (EOS) of Ta for bcc, fcc, and hcp crystal structures for pressures up to ∼500 GPa, and (ii) elastic ...

Four different force fields are examined for dynamic characteristics using cholesterol as a case study. The extent to which various types of internal degrees of freedom become thermodynamically relevant is evaluated by means of principal component analysis. More complex degrees of freedom (angle bending, dihedral rotations) show a trend towards force field independence. Moreover, charge assignm...

Long timescale (>1 micros) molecular dynamics simulations of protein folding offer a powerful tool for understanding the atomic-scale interactions that determine a protein's folding pathway and stabilize its native state. Unfortunately, when the simulated protein fails to fold, it is often unclear whether the failure is due to a deficiency in the underlying force fields or simply a lack of suff...

Assessment of chemical properties can often require a computationally costly sampling of a high-dimensional phase space in order accurately to predict ensemble-averaged values. Molecular mechanics simulations offer an efficient way to sample such ensembles, with the quality of the results depending on the ability of the force field adequately to describe the energetics of the system under the c...

Adri C. T. van Duin,†,| Siddharth Dasgupta,‡ Francois Lorant,§ and William A. Goddard III*,‡ Department of Fossil Fuels and EnVironmental Geochemistry, Drummond Building, UniVersity of Newcastle, Newcastle upon Tyne NE1 7RU, United Kingdom, Materials and Process Simulation Center, Beckman Institute (139-74), DiVision of Chemistry and Chemical Engineering, California Institute of Technology, Pas...

Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters for main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameter...

Effect of interparticle force on the hydrodynamics of gas-solid fluidized beds was investigated using the combined method of computational fluid dynamics and discrete element method (CFD-DEM). The cohesive force between particles was considered to follow the van der Waals equation form. The model was validated by experimental results from literature in terms of bed voidage distribution and Eule...

In this contribution we introduce the technical concept and implementation details concerning the front end of our force-field optimization workflow package for intramolecular degrees of freedom, called Wolf2Pack. The package's design follows our belief that parameter optimization should be a user-driven, but program guided, workflow with specific modular tasks that reduce human errors and save...

The overall objective in defining feature space is to reduce the dimensionality of the original pattern space, whilst maintaining discriminatory power for classification. To meet this objective in the context of ear biometrics a new force field transformation treats the image as an array of mutually attracting particles that act as the source of a Gaussian force field. Underlying the force fiel...