Related papers: Structure optimization in an off-lattice protein m…
Designing proteins with desired functions or properties represents a core goal in synthetic biology and drug discovery. Recent advances in protein language models (PLMs) have enabled the generation of highly designable protein sequences,…
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…
We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature…
Fermions and hardcore bosons share the same restriction: no more than one particle can occupy a single site in a lattice system. Specifically, in one dimension, two systems can share the same matrix representation. In this work, we…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
Using a fast tree-searching algorithm and a Pentium cluster, we enumerated all the sequences and compact conformations (structures) for a protein folding model on a cubic lattice of size $4\times3\times3$. We used two types of amino acids…
Large pretrained language models have transformed natural language processing, and their adaptation to protein sequences -- viewed as strings of amino acid characters -- has advanced protein analysis. However, the distinct properties of…
We discuss an efficient approach to the calculation of the internal energy in numerical simulations of spin systems with long-range interactions. Although, since the introduction of the Luijten-Bl\"ote algorithm, Monte Carlo simulations of…
We present an overview of the correlation-matrix methods developed recently by the CSSM Lattice Collaboration for the isolation of excited states of the nucleon. Of particular interest is the first positive-parity excited-state of the…
The recently developed stochastic gradient method combined with Monte Carlo sampling techniques [PRB {\bf 95}, 195154 (2017)] offers a low scaling and accurate method to optimize the projected entangled pair states (PEPS). We extended this…
We propose a novel method to optimize existing force-field parameters for protein systems. The method consists of minimizing the summation of the square of the force acting on each atom in the proteins with the structures from the Protein…
We apply the extended (statistically-consistent, SGA) Gutzwiller-type approach to the periodic Anderson model (PAM) in an applied magnetic field and in the strong correlation limit. The finite-U corrections are included systematically by…
We exploit the common mathematical structure of the numerical renormalization group and the density matrix renormalization group, namely, matrix product states, to implement an efficient numerical treatment of a two-lead, multi-level…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
We study the problem of three ultracold fermions in different hyperfine states loaded into a lattice with spatial dimension D=1,2. We consider SU(3)-symmetric attractive interactions and also eventually include a three-body constraint,…
We introduce a method based on semidefinite programming that produces rigorous two-sided bounds on ground state energy densities and correlation functions of translation-invariant classical spin models on infinite lattices. In this method,…
We revisit the old problem of which is the best single particle basis to express a Hubbard-like lattice model. A rigorous variational solution of this problem leads to equations in which the answer depends in a self-consistent manner on the…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…