Related papers: Fine structures of Intrinsically Disordered Protei…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Strongly interacting particles in one dimension subject to external confinement have become a topic of considerable interest due to recent experimental advances and the development of new theoretical methods to attack such systems. In the…
The well known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of…
Protein function is executed at the molecular surface, where shape and chemistry act together to govern interaction. Yet most comparison methods treat these aspects separately, privileging either global fold or local descriptors and missing…
Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors-tools that enable us to detect both the very large, such as the…
Liquid-liquid phase separation of charge/aromatic-enriched intrinsically disordered proteins (IDPs) is critical in the biological function of membraneless organelles. Much of the physics of this recent discovery remains to be elucidated.…
Interfaces have long been known to be the key to many mechanical and electric properties. To nickel base superalloys which have perfect creep and fatigue properties and have been widely used as materials of turbine blades, interfaces…
We examine five different popular rigid water models (SPC, SPCE, TIP3P, TIP4P and TIP5P) using MD simulations in order to investigate the hydrophobic hydration and interaction of apolar Lennard-Jones solutes as a function of temperature in…
To comprehend the complexities of the ice-water interface, we perform a study that attempts to correlate the altered dynamics of water to its perturbed structure at, and due to, the interface. The deviation from bulk values of structural…
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…
The accurate simulation of complex biochemical phenomena has historically been hampered by the computational requirements of high-fidelity molecular-modeling techniques. Quantum mechanical methods, such as ab initio wave-function (WF)…
A systematic global investigation of pairing properties based on all available experimental data on pairing indicators has been performed for the first time in the framework of covariant density functional theory. It is based on separable…
Through extensive molecular simulations we determine a phase diagram of attractive, flexible polymer chains in two and three dimensions. A surprisingly rich collection of distinct crystal morphologies appear, which can be finely tuned…
Computer simulations show that liquids of molecules with harmonic intramolecular bonds may have "pseudoisomorphic" lines of approximately invariant dynamics in the thermodynamic phase diagram. We demonstrate that these lines can be…
Each and every biological function in living organism happens as a result of protein-protein interactions.The diseases are no exception to this. Identifying one or more proteins for a particular disease and then designing a suitable…
Characterizing topological phases for strongly interacting fermions in the mixed-state regime remains a major challenge. Here we introduce a general and numerically efficient framework to diagnose mixed-state topological phases in strongly…
We investigate interfacial properties between two highly incompatible polymers of different stiffness. The extensive Monte Carlo simulations of the binary polymer melt yield detailed interfacial profiles and the interfacial tension via an…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
Background: Inelastic proton scattering at energies of a few hundred MeV and very-forward angles including $0^\circ$ has been established as a tool to study electric-dipole strength distributions in nuclei. The present work reports a…
The immersed peridynamics (IPD) method is a fluid-structure interaction (FSI) model to simulate fluid-driven material damage and failure of an immersed structure, in which a peridynamic (PD) constitutive correspondence model is employed…