Related papers: Contact-Density Analysis of Lattice Polymer Adsorp…
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…
For a class of nonequilibrium systems, called driven lattice gases, we study what happens when two systems are kept in contact and allowed to exchange particles with the total number of particles conserved. Both for attractive and repulsive…
In dense, static, polydisperse granular media under isotropic pressure, the probability density and the correlations of particle-wall contact forces are studied. Furthermore, the probability density functions of the populations of pressures…
In this paper we investigate the dynamical behavior of an interface or polymer, in interaction with a distant attractive substrate. The interface is modeled by the graph of a nearest neighbor path with non-negative integer coordinates, and…
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the…
We reassess the relation between classical lattice dimer models and the continuum elastic description of a lattice of fluctuating polymers. In the absence of randomness we determine the density and line tension of the polymers in terms of…
In Part I of this two part series, we presented a multi-neighbor dependent contact model for adhesive elastic-plastic particles built upon the method of dimensionality reduction that is valid for the elastic and fully-plastic contact…
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 present here exact results for a one-dimensional gas, or fluid, of hard-sphere particles with attractive boundaries. The particles, which can exchange with a bulk reservoir, mediate an interaction between the boundaries. A…
We consider forces acting on objects immersed in, or attached to, long fluctuating polymers. The confinement of the polymer by the obstacles results in polymer-mediated forces that can be repulsive (due to loss of entropy) or attractive (if…
The research is important for a molecular theory of liquid and has a wide interest as an example solving the problem when dynamic parameters of systems can be indirectly connected with their equilibrium properties. In frameworks of the…
We develop a mesoscopic lattice model to study the morphology formation in interacting ternary mixtures with evaporation of one component. As concrete application of our model, we wish to capture morphologies as they are typically arising…
We study the adsorption and desorption kinetics of interacting particles moving on a one-dimensional lattice. Confinement is introduced by limiting the number of particles on a lattice site. Adsorption and desorption are found to proceed at…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
We consider a system of particles interacting via a purely repulsive, soft-core potential recently introduced to model effective pair interactions between dendrimers, which is expected to lead to the formation of crystals with multiple…
Biopolymers are characterized by heterogeneous interactions, and usually perform their biological tasks forming contacts within domains of limited size. Combining polymer theory with a replica approach, we study the scaling properties of…
Elastic properties and internal states of isotropic sphere packings are studied by numerical simulations. Several numerical protocols to assemble dense configurations are compared. One, which imitates experiments with lubricated contacts,…
Interfacial properties of colloid--polymer mixtures are examined within an effective one--component representation, where the polymer degrees of freedom are traced out, leaving a fluid of colloidal particles interacting via polymer--induced…
We consider the entropy of polydisperse chains placed on a lattice. In particular, we study a model for equilibrium polymerization, where the polydispersivity is determined by two activities, for internal and endpoint monomers of a chain.…
We review the properties of reduced density matrices for free fermionic or bosonic many-particle systems in their ground state. Their basic feature is that they have a thermal form and thus lead to a quasi-thermodynamic problem with a…