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

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.


Diagram for chemical reaction example.Φ(1,3),1 and Φ(2,5),1 represent the stable bonds AB and AC, respectively. The dashed lines represent the repulsion forces induced by the encoding functions. (a) the repulsion between A and C is due to the partial derivatives of  with respect to both x2 and x5. (b) the repulsion between A and B is due to the partial derivatives of  with respect to both x1 and x3. See Supplementary Information Sec. III.A for a discussion of the repulsion force induced by the smooth encoding functions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5037383&req=5

f6: Diagram for chemical reaction example.Φ(1,3),1 and Φ(2,5),1 represent the stable bonds AB and AC, respectively. The dashed lines represent the repulsion forces induced by the encoding functions. (a) the repulsion between A and C is due to the partial derivatives of with respect to both x2 and x5. (b) the repulsion between A and B is due to the partial derivatives of with respect to both x1 and x3. See Supplementary Information Sec. III.A for a discussion of the repulsion force induced by the smooth encoding functions.

Mentions: This example makes use of the multiplicity function in (2) in order to model the electron-electron repulsion during the transition state. It also shows that the use of a smooth encoding function accurately accounts for the bond dissociation energy. Let be the configuration vector for this system (see Fig. 6).


Programmable Potentials: Approximate N-body potentials from coarse-level logic
Diagram for chemical reaction example.Φ(1,3),1 and Φ(2,5),1 represent the stable bonds AB and AC, respectively. The dashed lines represent the repulsion forces induced by the encoding functions. (a) the repulsion between A and C is due to the partial derivatives of  with respect to both x2 and x5. (b) the repulsion between A and B is due to the partial derivatives of  with respect to both x1 and x3. See Supplementary Information Sec. III.A for a discussion of the repulsion force induced by the smooth encoding functions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Diagram for chemical reaction example.Φ(1,3),1 and Φ(2,5),1 represent the stable bonds AB and AC, respectively. The dashed lines represent the repulsion forces induced by the encoding functions. (a) the repulsion between A and C is due to the partial derivatives of with respect to both x2 and x5. (b) the repulsion between A and B is due to the partial derivatives of with respect to both x1 and x3. See Supplementary Information Sec. III.A for a discussion of the repulsion force induced by the smooth encoding functions.
Mentions: This example makes use of the multiplicity function in (2) in order to model the electron-electron repulsion during the transition state. It also shows that the use of a smooth encoding function accurately accounts for the bond dissociation energy. Let be the configuration vector for this system (see Fig. 6).

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.