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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.


Simple DNA transcription model.Free base nucleotides cannot bind with the DNA strand until RNA pol binds with the promoter. When RNA pol is bound to the promoter, the free nucleotides bind to the DNA strand ACTG sequentially from left to right. Once the complementary strand has formed, the RNA pol unbinds from the promoter and then the complementary strand can diffuse away. Once the RNA pol has diffused far enough away, the bonds between the complementary base pairs turn off and the complementary strand can diffuse away. Dashed arrows between sites denotes an active potential. The P blocks denote a phosphate group and the S blocks denote a sugar group.
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f10: Simple DNA transcription model.Free base nucleotides cannot bind with the DNA strand until RNA pol binds with the promoter. When RNA pol is bound to the promoter, the free nucleotides bind to the DNA strand ACTG sequentially from left to right. Once the complementary strand has formed, the RNA pol unbinds from the promoter and then the complementary strand can diffuse away. Once the RNA pol has diffused far enough away, the bonds between the complementary base pairs turn off and the complementary strand can diffuse away. Dashed arrows between sites denotes an active potential. The P blocks denote a phosphate group and the S blocks denote a sugar group.

Mentions: The final example is inspired by DNA transcription2728. The model consists of a promoter region (sites 1 and 2) to which RNA polymerase (RNA pol) binds (sites 3 and 4), and a four nucleotide DNA strand, ACTG, to be transcribed (Fig. 10). As a first approximation of the transcription process, the movement of the RNA polymerase down the DNA chain and the unwinding/rewinding of the DNA have not been explicitly modeled.


Programmable Potentials: Approximate N-body potentials from coarse-level logic
Simple DNA transcription model.Free base nucleotides cannot bind with the DNA strand until RNA pol binds with the promoter. When RNA pol is bound to the promoter, the free nucleotides bind to the DNA strand ACTG sequentially from left to right. Once the complementary strand has formed, the RNA pol unbinds from the promoter and then the complementary strand can diffuse away. Once the RNA pol has diffused far enough away, the bonds between the complementary base pairs turn off and the complementary strand can diffuse away. Dashed arrows between sites denotes an active potential. The P blocks denote a phosphate group and the S blocks denote a sugar group.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f10: Simple DNA transcription model.Free base nucleotides cannot bind with the DNA strand until RNA pol binds with the promoter. When RNA pol is bound to the promoter, the free nucleotides bind to the DNA strand ACTG sequentially from left to right. Once the complementary strand has formed, the RNA pol unbinds from the promoter and then the complementary strand can diffuse away. Once the RNA pol has diffused far enough away, the bonds between the complementary base pairs turn off and the complementary strand can diffuse away. Dashed arrows between sites denotes an active potential. The P blocks denote a phosphate group and the S blocks denote a sugar group.
Mentions: The final example is inspired by DNA transcription2728. The model consists of a promoter region (sites 1 and 2) to which RNA polymerase (RNA pol) binds (sites 3 and 4), and a four nucleotide DNA strand, ACTG, to be transcribed (Fig. 10). As a first approximation of the transcription process, the movement of the RNA polymerase down the DNA chain and the unwinding/rewinding of the DNA have not been explicitly modeled.

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.