Related papers: Stability Threshold as a Selection Principle for P…

The limiting stability of invariant probability measures of time homogeneous transition semigroups for autonomous stochastic systems has been extensively discussed in the literature. In this paper we initially initiate a program to study…

We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…

Feature selection, as a vital dimension reduction technique, reduces data dimension by identifying an essential subset of input features, which can facilitate interpretable insights into learning and inference processes. Algorithmic…

Algorithms for machine learning-guided design, or design algorithms, use machine learning-based predictions to propose novel objects with desired property values. Given a new design task -- for example, to design novel proteins with high…

Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to…

Machine learning-based design has gained traction in the sciences, most notably in the design of small molecules, materials, and proteins, with societal implications spanning drug development and manufacturing, plastic degradation, and…

We propose and discuss a novel strategy for protein design. The method is based on recent theoretical advancements which showed the importance to treat carefully the conformational free energy of designed sequences. In this work we show how…

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…

We study stable matchings that are robust to preference changes in the two-sided stable matching setting of Gale and Shapley [GS62]. Given two instances $A$ and $B$ on the same set of agents, a matching is said to be robust if it is stable…

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…

We propose a new and effective means for designing stable and fast-folding polypeptide sequences using a cumulant expansion of the molecular partition function. This method is unique in that $T_{Z}$, the ``cumulant design temperature''…

Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…

An efficient numerical framework is presented for modeling viscoelasticity and permanent set of polymers. It is based on the hereditary integral form of transient network theory, in which polymer chains belong to distinct networks each with…

Various genome evolutionary models have been proposed these last decades to predict the evolution of a DNA sequence over time, essentially described using a mutation matrix. By essence, all of these models relate the evolution of DNA…

Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…

Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…

Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…

Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…

We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…