Related papers: Comparative analysis of rigidity across protein fa…
Protein-nucleic acid complexes are important for many cellular processes including the most essential function such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…
We study an elasticity model for compressed protein monolayers or particle rafts at a liquid interface. Based on the microscopic view of hard-core particles with soft shells, a bead-spring model is formulated and analyzed in terms of…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
It is established that the mechanical properties of hydrogels control the fate of (stem) cells. However, despite its importance, a one-to-one correspondence between gels' stiffness and cell behaviour is still missing from literature. In…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Shear thickening suspensions of non-Brownian polydisperse particles are simulated in 2D using a discrete element method based algorithm (LF-DEM) at high packing fractions ($\phi$) and large non-dimensional stresses ($\sigma$). Rigidity…
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…
Conformational properties of polymer melts confined between two hard structureless walls are investigated by Monte Carlo simulation of the bond-fluctuation model. Parallel and perpendicular components of chain extension, bond-bond…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
Gelatin is often used as an analog for studying soft and biological materials in order to understand the mechanics of behavior of biological tissue in events like traumatic brain injuries. The material properties of gelatin change with the…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts with other sites in a structure have been shown to evolve more…
Differential shrinkage in particulate quasi-brittle materials causes microcracking which reduces durability in these materials by increasing their mass transport properties. A hydro-mechanical three-dimensional periodic network approach was…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
Determining the onset of rigidity in gels is a fundamental challenge with significant practical implications across different applications. Limited-valence, or patchy-particle systems have proven to be a valuable model to study the…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…