Force field (chemistry) | EPFL Graph Search

In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates. All-atom force fields provide parameters for every type of atom in a system, inc

Carbon Nanotubes

Jaap Kroes

This thesis studies carbon nanotubes using state-of-the-art computational methods. Using large-scale quantum-mechanical calculations, based on density-functional-theory, we investigate several important aspects of the physics and chemistry of single-walled-nanotubes. The focus is on the effect of defects, namely adparticles and vacancies, on the structural, electronic and dynmical properties of the nanotubes. We also present preliminary results of simulations exploring a possible route for the formation of SWNTs from graphene nanoflakes. Adparticles include atomic hydrogen, oxygen, sulfur at different concentrations as well as nitrogen--oxides. Chemisorption of hydrogen as well as oxygen and isoelectronic species results in the formation of clusters on the sidewall, with characteristic structures corresponding to characteristic signatures in the electronic spectra. Especially in the case of oxygen, we find that relatively high energy barriers separate different structures: this shows that not only thermodynamically favored configurations are relevant for the understanding of oxygen chemisorption but the presence of traps cannot be neglected. The fingerpint of these traps is confirmed by scanning-tunneling spectroscopy. Trends with size and chirality of the nanotubes and oxygen coverage are studied in detail and also explained in terms of simple chemical descriptors. The importance of large-scale atomistic models is also emphasized to obtain convergent results and thus reliable predictions, and comparison is made of results we obtain using different gradient-corrected exchange-correlation functionals and in part with hybrid functionals. The study of nitrogen-oxides faces the difficulty to correctly represent physisorption, also with empirically corrected gradient-corrected exchange-correlation and hybrid functionals. Still our calculations of vibrational frequencies of different molecules on the sidewall, once compared with experiment, are able to distinguish the specific species observed in infrared spectra. Part of our work is centered on the comparison of widely used classical potentials (reactive force fields) with DFT results. Specifically we use them to study hydrogen and oxygen chemisorption, and especially examine the validity of several different force-fields for the description of the structure and energetics of single and double vacancies. In all cases, we find rather limited agreement with DFT results, showing the intrinsic difficulty to represent the subtle and intrinsic quantum effects governing the physico-chemical behavior of carbon nanotubes. Still, the wealth of results we have obtained might be useful for an improvement of these classical schemes for a specific application or other semi-classical models.

EPFL2014

Accelerating materials discovery for solid state electrolytes

Matthieu Gilles Mottet

The development of new solid-state electrolytes is a key step in improving the performance and safety of battery technology. Although the use of first-principle methods has proved invaluable in better understanding the process at play in these materials, these methods remains extremely costly and limit the ability to model the diffusion phenomena as this one is often happening over large time-scales. To solve this issue and unlock larger time-scale and supercells, the use of force-fields has proven to be a effective solution. In particular, polarizable force-fields have been shown to be effective at reproducing accurate diffusion results. To this effect, a methodology is proposed here for the training of such polarizable force-fields using a Self-Adaptive Differential Evolution algorithm. The constant optimization of the shell positions is avoided by using its optimal position with respect to the error on cores. Furthermore, the generation of synthetic training sets is proposed through the use of Monte-Carlo dynamics and random thermal displacements. The potential of force-field modeling is then demonstrated by investigating the effect of tungsten doping on garnet type electrolytes. This investigation shows the importance of averaging over dopant distributions and highlights the complex interplay between the various effects resulting of the insertion of doping species. These various effects are isolated through the use of two distinct doping models, an implicit model where the extra positive charge is introduced as a background charge and an explicit one where the dopant is explicitly introduced. Finally the computation of the electrochemical stability of solid-state electrolytes is introduced. The different methods used to compute it are discussed and their results for relevant Li- and Na-based solid-state electrolytes are compared.

EPFL2020

Field-based Strategies for Solid-Liquid Separation

Thierry Chappuis

The ever increasing demand for large quantities of bio-engineered pharmaceuticals and the tendency for doses to become larger stimulate the development of more productive and reliable mammalian cell culture technologies. In this context, perfusion bioreactors appear an efficient means to achieve high volumetric productivity and high product concentration. Since large-scale implementation of perfusion is limited by the reliability and scale-up potential of the device used to achieve cell retention, the present work proposes to tackle the problem bottom-up from the fundamentals of physics in order to develop, characterize and model novel particle retention strategies able to overcome the limitations of state-of-the-art systems. The first part of the present thesis focuses on the identification of physical force fields chosen for their ability to drive particles or cells into highly localized regions of a suspension. The ability of ultrasonic, dielectrophoretic and magnetophoretic interactions to make cells levitate over a surface was identified as an innovative way of implementing a Boycott effect (similar to that occurring in inclined sedimentation channels) while maintaining the flow channel in a vertical position. Therefore, inclined settlers were chosen as a reference system and the Ponder-Nakamura-Kuroda theory describing their performance was extended to take into account ultrasonic, dielectrophoretic and magnetic effects. The second part of the work provides deep modeling insight into the mechanisms underlying mammalian cell retention in these new filter implementations. Potentials and limitations are discussed in details. In particular, coupling dielectrophoresis with the Boycott effect proved to be successful in separating polystyrene particles from their moderately electrically conductive suspending medium. However, in highly conductive media, this process was shown to be very sensitive to order-disruptive electrokinetic effects such as ac electroosmosis and electrothermal fluid flow. Heat dissipation is however not specific to dielectrophoresis. This phenomenon is also a known limitation of the ultrasonic or magnetophoretic implementations, in certain conditions. The last part focused its work on the development of magnetophoretically-enhanced sedimentation, which was proposed as a means to partly overcome the heat dissipation problem observed with dielectrophoresis in highly conductive culture media. For such a magnetic approach to work correctly with intrinsically nonmagnetic materials, a paramagnetic suspending medium has to be used. The current implementation proposes to prepare media with fair quantities of gadolinium(III) or dysprosium(III) salts dissolved in them. Using such a paramagnetic buffer, the feasibility of magnetically retaining polystyrene particles could be verified in a vertical separation channel, hence providing first demonstration of the principle. The use of paramagnetic substances in mammalian cell culture media is naturally a matter of concern. The present work addresses this question as well and highlights the feasibility of growing Chinese Hamster Ovary cells in Gd(III)- or Dy(III)-rich environments. In contrast, attempts to develop low electrically conductive culture media failed and replacement of the NaCl content by D-mannitol or glycerol demonstrated severe growth inhibition effects.

EPFL2010