相关论文: Coarse-Grained Residue-Based Models of Disordered …

This article focuses on phase and aggregation behavior for linear chains composed of blocks of hydrophilic and hydrophobic segments. Phase and conformational transitions of patterned chains are relevant for understanding liquid-liquid…

We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained (CG) bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional…

Elastin-like polypeptides (ELPs) undergo a sharp solubility transition from low temperature solvated phases to coacervates at elevated temperatures, driven by the increased strength of hydrophobic interactions at higher temperatures. The…

We investigate liquid-liquid phase separation (LLPS) and interfacial properties of two LLPS modes: associative (ALLPS) and segregative (SLLPS). Analytical expressions for the critical point (CP) and binodal boundaries are derived and show…

Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…

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…

Living systems must maintain robust biochemical function despite fluctuations that span a wide range of timescales. Biomolecular condensates formed by liquid-liquid phase separation (LLPS) have been shown to buffer concentration…

Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…

Liquid liquid phase separation (LLPS) of proteins is an intracellular process that is widely used by cells for many purposes. In living cells (in vivo), LLPS occurs in complex and crowded environments. Amino acids (AAs) are vital components…

Biomolecular phase separation is typically attributed to the polymer physics of long, disordered chains. However, the underlying chemical grammar, i.e. the specific interactions between protein and RNA building blocks, remains poorly…

Liquid-liquid phase separation is the mechanism underlying the formation of biomolecular condensates. Disordered protein regions often drive phase separation, but molecular interactions of disordered protein regions are not well understood,…

Sequential or online dimensional reduction is of interests due to the explosion of streaming data based applications and the requirement of adaptive statistical modeling, in many emerging fields, such as the modeling of energy end-use…

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…

Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…

In this paper, we construct protograph-based spatially coupled low-density parity-check (SC-LDPC) codes by coupling together a series of L disjoint, or uncoupled, LDPC code Tanner graphs into a single coupled chain. By varying L, we obtain…

We use a standard bead-spring model and molecular dynamics simulations to study the static properties of symmetric linear multiblock copolymer chains and their blocks under poor solvent conditions in a dilute solution from the regime close…

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…

Lattice models are crucial for studying thermodynamic properties in many physical, biological and chemical systems. We investigate Lattice Restricted Primitive Model (LRPM) of electrolytes with different discretization parameters in order…

Spatially coupled codes have been shown to universally achieve the capacity for a large class of channels. Many variants of such codes have been introduced to date. We discuss a further such variant that is particularly simple and is…

We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules.…