Related papers: Lattice models for protein organization throughout…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
This paper investigates the structure-property relations of thin-walled lattices under dynamic longitudinal compression, characterized by their cross-sections and heights. These relations elucidate the interactions of different geometric…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We perform an analytical investigation of the cell interface dynamics in the framework of a minimal phase field model of cell motility suggested in [1], which consists of two coupled evolution equations for the order parameter and a…
Much of our understanding of the physical properties of raft domains in biological membranes, and some insight into the mechanisms underlying their formation stem from atomistic simulations of simple model systems, especially ternary…
In this paper, we introduce a three-dimensional mathematical model of collagen contraction with microbuckling based on the two-dimensional model previously developed by the authors. The model both qualitatively and quantitatively replicates…
We study the transport and localization properties of scalar vibrations on a lattice with random bond strength by means of the transfer matrix method. This model has been recently suggested as a means to investigate the vibrations and heat…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
We analyze response of a macromolecule near to a substrate; the substrate is tiled in the sequential and specific manner so that repeat units of the macromolecule may have different response on its adsorption in different directions onto…
Predicting how materials behave under realistic conditions requires understanding the statistical distribution of atomic configurations on crystal lattices, a problem central to alloy design, catalysis, and the study of phase transitions.…
It is crucial to measure position and conformational changes of a membrane-interacting protein relative to the membrane surface. This is however challenging because the thickness of a membrane is usually only about 4 nm. We developed a…
Lattice models or structures are geometrical objects with mathematical forms, that are used to represent physical systems. They have been used widely in diverse fields, namely, in condensed matter physics, to study degrees of freedom of…
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…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
A crystal lattice, when confined to the surface of a cylinder, must have a periodic structure that is commensurate with the cylinder circumference. This constraint can frustrate the system, leading to oblique crystal lattices or to…