相关论文: Structure optimization in an off-lattice protein m…

We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…

A new variational method is developed to calculate the ground state energy of Fermi systems with strong short-range correlations. A trial wave function of Gutzwiller's type contains additional variational parameters corresponding to…

We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method…

We investigate the competition between attractive spin-spin interactions and spin-separating external forces in the ground state of a one-dimensional Fermi-Hubbard model. We consider a lattice with open boundary conditions, subject to a…

Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…

We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…

Understanding how a stressor applied on a biological system shapes its evolution is key to achieving targeted evolutionary control. Here we present a toy model of two interacting lattice proteins to quantify the response to the selective…

For various two dimensional lattices such as honeycomb, kagome, and square-octagon, gauge conventions (string gauge) realizing minimum magnetic fluxes that are consistent with the lattice periodicity are explicitly given. Then many-body…

We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…

We present ground state calculations for low-density Fermi gases described by two model interactions, an attractive square-well potential and a Lennard-Jones potential, of varying strength. We use the optimized Fermi-Hypernetted Chain…

We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…

We consider pairwise interaction energies and we investigate their minimizers among lattices with prescribed minimal vectors (length and coordination number), i.e. the one corresponding to the crystal's bonds. In particular, we show the…

An improved particle swarm optimization algorithm is proposed and its superiority over standard particle swarm optimization algorithm is tested on two typical benchmark functions. By employing this algorithm to search for the magnetic…

The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model…

Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…

Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…

Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…

Single partially confined collapsed polymers are studied in two dimensions. They are described by self-avoiding random walks with nearest-neighbour attractions below the $\Theta$-point, on the surface of an infinitely long cylinder. For the…

Continuous-Time Quantum Monte Carlo (CT-QMC) method combined with Dynamical Mean Field Theory (DMFT) is used to calculate both Periodic Anderson Model (PAM) and Kondo Lattice Model (KLM). Different parameter sets of both models are…

Strongly-interacting ultra-cold atoms in tight-binding optical lattice potentials provide an ideal platform to realize the fundamental Hubbard model. Here, after outlining the elementary single particle solution, we review and expand our…