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Programmable Potentials: Approximate N-body potentials from coarse-level logic

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ABSTRACT

This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the “coefficients” of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.

No MeSH data available.


The two most probable outcomes of a successful AB + C event.Both trajectories start at the same configuration the difference is that C has a greater momentum for the blue (thicker) curved arrow. For both the red and blue trajectories, C approaches A. The AB bond breaks when . Depending on the momentum and the relative strength of the repulsion terms, either AB reforms or AC forms.
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f7: The two most probable outcomes of a successful AB + C event.Both trajectories start at the same configuration the difference is that C has a greater momentum for the blue (thicker) curved arrow. For both the red and blue trajectories, C approaches A. The AB bond breaks when . Depending on the momentum and the relative strength of the repulsion terms, either AB reforms or AC forms.

Mentions: There are three possible outcomes for when the system exits its transition state: (i) either AC forms a stable molecule, (ii) AB reforms, or (iii) no bonds are formed and all the molecules are free molecules. This depends on the equilibrium distances of the bonds, the dissociation distances, the incoming momentum of C, and the repulsion forces. Figure 7 shows the two most probable outcomes for a single AB + C event.


Programmable Potentials: Approximate N-body potentials from coarse-level logic
The two most probable outcomes of a successful AB + C event.Both trajectories start at the same configuration the difference is that C has a greater momentum for the blue (thicker) curved arrow. For both the red and blue trajectories, C approaches A. The AB bond breaks when . Depending on the momentum and the relative strength of the repulsion terms, either AB reforms or AC forms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037383&req=5

f7: The two most probable outcomes of a successful AB + C event.Both trajectories start at the same configuration the difference is that C has a greater momentum for the blue (thicker) curved arrow. For both the red and blue trajectories, C approaches A. The AB bond breaks when . Depending on the momentum and the relative strength of the repulsion terms, either AB reforms or AC forms.
Mentions: There are three possible outcomes for when the system exits its transition state: (i) either AC forms a stable molecule, (ii) AB reforms, or (iii) no bonds are formed and all the molecules are free molecules. This depends on the equilibrium distances of the bonds, the dissociation distances, the incoming momentum of C, and the repulsion forces. Figure 7 shows the two most probable outcomes for a single AB + C event.

View Article: PubMed Central - PubMed

ABSTRACT

This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the “coefficients” of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.

No MeSH data available.