Design Equation: A Novel Approach to Heteropolymer Design
Yukito Iba (The Institute of Statistical Mathematics), Macoto Kikuchi, (Osaka University), Kei Tokita (Harvard University, Permanent Address:Osaka, University)
TL;DR
This paper introduces a new heteropolymer design method using soft spins and a design equation inspired by Boltzmann machine learning, demonstrated on a 3x3x3 lattice model.
Contribution
It presents a novel design equation for heteropolymers based on fuzzy monomers, extending the Kurosky and Deutsch criterion, with an implementation for lattice models.
Findings
Effective heteropolymer design algorithm developed
Algorithm performs well on 3x3x3 lattice model
Introduces soft spins for improved design flexibility
Abstract
A novel approach to heteropolymer design is proposed. It is based on the criterion by Kurosky and Deutsch, with which the probability of a target conformation in a conformation space is maximized at low but finite temperature. The key feature of the proposed approach is the use of soft spins (fuzzy monomers) that leads to a design equation, which is an analog of the Boltzmann machine learning equation in the design problem. We implement an algorithm based on the design equation for the generalized HP model on the 3x3x3 cubic lattice and check its performance.
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