Related papers: Quinary lattice model of secondary structures of p…
We present a new ternary free energy lattice Boltzmann model. The distinguishing feature of our model is that we are able to analytically derive and independently vary all fluid-fluid surface tensions and the solid surface contact angles.…
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…
We study a new class of matrix models, formulated on a lattice. On each site are $N$ states with random energies governed by a Gaussian random matrix Hamiltonian. The states on different sites are coupled randomly. We calculate the density…
With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
We discuss a series of 8 energy scales, some of which just speculated by ourselves, and fit the logarithms of these energies as a straight line versus a quantity related to the dimensionalities of action terms in a way to be defined in the…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
We propose a lattice density-functional theory for {\it ab initio} quantum chemistry or physics as a route to an efficient approach that approximates the full configuration interaction energy and orbital occupations for molecules with…
We present a general procedure for constructing lattices of qubits with a Hamiltonian composed of nearest-neighbour two-body interactions such that the ground state encodes a cluster state. We give specific details for lattices in one-,…
Several UV complete models of physics beyond the Standard Model are currently under scrutiny, their low-energy dynamics being compared with the experimental data from the LHC. Lattice simulations can play a role in these studies by…
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding…
We analyze the crystallization and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer…
We consider a binary mixture of colloid and polymer particles with positions on a simple cubic lattice. Colloids exclude both colloids and polymers from nearest neighbor sites. Polymers are treated as effective particles that are mutually…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
We have constructed a model for the kinetics of rupture of membranes under tension, applying physical principles relevant to lipid bilayers held together by hydrophobic interactions. The membrane is characterized by the bulk compressibility…
Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and…
Recently, a new connection between density functional theory and kinetic theory has been proposed. In particular, it was shown that the Kohn-Sham (KS) equations can be reformulated as a macroscopic limit of the steady-state solution of a…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real…
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…