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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.


One realization of the inhibitor molecule system (11) simulated in LAMMPS.Initially, the AB complex is formed. Around 30 femtoseconds (fs) C comes close enough, turns off the AB bond and BC forms and can diffuse away from A. This remains the case until around 450 fs, when A approaches BC, the BC bond turns off and the AC bond turns on.
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f5: One realization of the inhibitor molecule system (11) simulated in LAMMPS.Initially, the AB complex is formed. Around 30 femtoseconds (fs) C comes close enough, turns off the AB bond and BC forms and can diffuse away from A. This remains the case until around 450 fs, when A approaches BC, the BC bond turns off and the AC bond turns on.

Mentions: Here, we are only interested in demonstrating the methodology qualitatively so we make the approximation that derivative of each encoding function is 0 almost everywhere (this would be the case if the logic functions were used in place of the encoding functions in (11). With this approximation the force only consists of terms of the form . One realization of the inhibitor molecule system (11) simulated in LAMMPS25 with this approximation is shown in Fig. 5. The potentials Φp are formed from Morse potentials


Programmable Potentials: Approximate N-body potentials from coarse-level logic
One realization of the inhibitor molecule system (11) simulated in LAMMPS.Initially, the AB complex is formed. Around 30 femtoseconds (fs) C comes close enough, turns off the AB bond and BC forms and can diffuse away from A. This remains the case until around 450 fs, when A approaches BC, the BC bond turns off and the AC bond turns on.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: One realization of the inhibitor molecule system (11) simulated in LAMMPS.Initially, the AB complex is formed. Around 30 femtoseconds (fs) C comes close enough, turns off the AB bond and BC forms and can diffuse away from A. This remains the case until around 450 fs, when A approaches BC, the BC bond turns off and the AC bond turns on.
Mentions: Here, we are only interested in demonstrating the methodology qualitatively so we make the approximation that derivative of each encoding function is 0 almost everywhere (this would be the case if the logic functions were used in place of the encoding functions in (11). With this approximation the force only consists of terms of the form . One realization of the inhibitor molecule system (11) simulated in LAMMPS25 with this approximation is shown in Fig. 5. The potentials Φp are formed from Morse potentials

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.