Related papers: Differential Effects of Sequence-Local versus Nonl…
We study the relationship between topological defect formation and ground-state packings in a model of repulsions in external confining potentials. Specifically we consider screened 2D Coulombic repulsions, which conveniently parameterizes…
Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex…
Polyampholyte field theory and explicit-chain molecular dynamics models of sequence-specific phase separation of a system with two intrinsically disordered protein (IDP) species indicate consistently that a substantial polymer excluded…
There is evidence for competition between superconductivity and short-range charge-density wave order in a number of cuprate compounds and especially in YBa$_2$Cu$_3$O$_{6+x}$. Here, we use a non-linear sigma model of such competition to…
Mathematical programs with complementarity constraints (MPCCs) are a challenging class of nonlinear optimization problems, because their nonlinear programming reformulations violate standard constraint qualifications at every feasible…
The mechanical response of intrinsically disordered proteins (IDPs) and polyampholyte (PA) chains is vital for understanding their biological functions and designing functional materials. We investigate the force-extension behavior of a PA…
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…
Effects of size and charge asymmetry between oppositely charged ions or particles on spatial inhomogeneities are studied for a large range of charge and size ratios. We perform a stability analysis of the primitive model (PM) of ionic…
We introduce the Korringa-Kohn-Rostocker non-local coherent potential approximation (KKR-NLCPA) for describing the electronic structure of disordered systems. The KKR-NLCPA systematically provides a hierarchy of improvements upon the widely…
It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a…
We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength $\kappa$ of the local…
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during…
Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we…
We consider a phantom chain model of polymer with internal friction in a harmonic confinement and extend it to take care of effects of solvent quality following a mean field approach where an exponent $\nu$ is introduced. The model termed…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
The disorder parameter, defined as the expectation value of the symmetry transformation acting on a subsystem, can be used to characterize symmetric phases as an analogy to detecting spontaneous symmetry breaking (SSB) phases using local…
Scanning tunneling spectroscopy experiments on a number of cuprate superconductors have revealed that these materials are highly inhomogeneous. However, even though this inhomogeneity is well-characterized experimentally, a theoretical…
The utilization and control of nonlocal quantum interactions is an area of active investigation. This is not limited to subatomic structures but extends to the macroscopic level. Nonlocal interactions can be from either entanglement or path…
Principal Component Analysis (PCA) is an important tool of dimension reduction especially when the dimension (or the number of variables) is very high. Asymptotic studies where the sample size is fixed, and the dimension grows [i.e., High…
We extend the single-site coherent potential approximation (CPA) to include the effects of non-local disorder correlations (alloy short-range order) on the electronic structure of random alloy systems. This is achieved by mapping the…