Related papers: Structure optimization in an off-lattice protein m…
By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the…
Single two dimensional polymers confined to a strip are studied by Monte Carlo simulations. They are described by N-step self-avoiding random walks on a square lattice between two parallel hard walls with distance 1 << D << N^\nu (\nu = 3/4…
We study harmonically trapped, unpolarized fermion systems with attractive interactions in two spatial dimensions with spin degeneracies Nf = 2 and 4 and N/Nf = 1, 3, 5, and 7 particles per flavor. We carry out our calculations using our…
Periodic Anderson model (PAM), where local electron orbitals interplay with itinerant electronic carriers, plays an essential role in our understanding on heavy fermion materials. Motivated by recent proposal of simulating Kondo lattice…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
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…
We study the ground state of the doped Hubbard model on the honeycomb lattice in the small doping and strongly interacting region. The nature of the ground state by doping holes into the anti-ferromagnetic Mott insulating states on the…
Simulating soft matter systems such as the cytoskeleton can enable deep understanding of experimentally observed phenomena. One challenge of modeling such systems is realistic description of the steric repulsion between nearby polymers.…
We introduce RosettaSearch, an inference-time multi-objective optimization approach for backbone conditioned protein sequence design. We use large language models (LLMs) as a generative optimizer within a search algorithm capable of…
The potential energy surface of an off-lattice model protein is characterized in detail by constructing a disconnectivity graph and by examining the organisation of pathways on the surface. The results clearly reveal the frustration…
We study the possible ground state configurations of two strongly coupled chains of charge neutral spin-3/2 fermionic atoms interacting via short range van der Waals interaction. The coupling between the two chains is realized by relatively…
In a recent contribution [Phys. Rev. B 81, 165104 (2010)] fermionic Projected Entangled-Pair States (PEPS) were used to approximate the ground state of free and interacting spinless fermion models, as well as the $t$-$J$ model. This paper…
We study Hubbard models for ultracold bosonic or fermionic atoms loaded into an optical lattice. The atoms carry a high spin $F>1/2$, and interact on site via strong repulsive Van der Waals forces. Making convenient rearrangements of the…
We investigate two-component ultracold fermionic atoms with repulsive interactions trapped in an optical lattice with a ladder structure. By applying the Bogoliubov-de Gennes equations to an effective t-J model in the strong correlation…
Incorporating the concept of order parameter of the mean-field theory into the simulated annealing method, we presented a new optimization algorithm, the guided simulated annealing method. In this method mean-field order parameters are…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions…
Projected entangled pair states (PEPS) on finite two-dimensional lattices are a natural ansatz for representing ground states of local many-body Hamiltonians, as they inherently satisfy the boundary law of entanglement entropy. In this…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…