Related papers: Lattice stretching bistability and dynamic heterog…
Moir\'e superlattices formed in stacks of two or more 2D crystals with similar lattice structures have recently become excellent platforms to reveal new physics in low-dimensional systems. They are, however, highly sensitive to the angle…
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two subdomains, by Monte Carlo simulations. A…
We consider a polaron model where molecular \emph{rotations} are important. Here, the usual hopping between neighboring sites is affected directly by the electron-phonon interaction via a {\em twist-dependent} hopping amplitude. This model…
The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding $\lambda$-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability and…
We investigate the existence of topological phases in a dense two-dimensional atomic lattice gas. The coupling of the atoms to the radiation field gives rise to dissipation and a non-trivial coherent long-range exchange interaction whose…
Ferrogels are smart soft materials, consisting of a polymeric network and embedded magnetic particles. Novel phenomena, such as the variation of the overall mechanical properties by external magnetic fields, emerge consequently. However,…
A model is presented to explain the normal mode features of dust particles in a planar zigzag crystal chain for the first and second neighbors. The degrees of freedom of particles are the longitudinal and transverse displacements in plane…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
The static potential in the confinement ``phase'' of the SU(2) Higgs model is studied. In particular, the observation of the screening (called string breaking) of the static quarks by the dynamical light quarks leading to the formation of…
The shape of a polymer plays an important role in determining its interactions with other molecules and with the environment, and is in turn affected by both of them. As a consequence, in the literature the shape properties of a chain in…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
Adhesive interactions between elastic structures such as graphene sheets, carbon nanotubes, and microtubules have been shown to exhibit hysteresis due to irrecoverable energy loss associated with bond breakage, even in static…
Viewed under a fluorescence microscope, the actomyosin cytoskeleton presents vivid streaks of lines together with persistent oscillatory waves. Using an active hydrodynamic approach, we show how a uniform distribution of single or mixture…
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…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $\theta$-temperature is predicted to be sharp. For…
We study localization driven solely by interparticle interactions in moir\'e lattice systems without intrinsic disorder or externally imposed quasiperiodic potentials. We consider a one-dimensional bilayer with incommensurate lattice…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Confinement is an ubiquitous phenomenon when matter couples to gauge fields, which manifests itself in a linear string potential between two static charges. Although gauge fields can be integrated out in one dimension, they can mediate…