arXiv subjects

Danqi Lang

Publications and source records attributed to Danqi Lang.

3 recordsLinked to original sources

arXiv2024

$NVU$ view on energy polydisperse Lennard-Jones systems

When energy polydispersity is introduced into the Lennard-Jones (LJ) system, there is little effect on structure and dynamics [Ingebrigtsen and Dyre, J. Phys. Chem. B 127, 2837 (2023)]. For instance, at a given state point both the radial distribution function and the mean-square displacement as a function of time are virtually unaffected by even large energy polydispersity, which is in stark contrast to what happens when size polydispersity is introduced. We here argue -- and validate by simulations of up to 30\% polydispersity -- that this almost invariance of structure and dynamics reflects an approximate invariance of the constant-potential-energy surface. Because $NVU$ dynamics defined as geodesic motion at constant potential energy is equivalent to Newtonian dynamics in the thermodynamic limit, the approximate invariance of the constant-potential-energy surface implies virtually the same physics of energy polydisperse LJ systems as of the standard single-component version. In contrast, the constant-potential-energy surface is significantly affected by introducing size polydispersity.

cond-mat.soft↗

arXiv2024

Anti-correlation between excitations and locally-favored structures in glass-forming systems

Dynamics that are microscopic in space and time, in which particles commit to a position, so-called excitations, are considered the elementary unit of relaxation in the Dynamic Facilitation (DF) theory of the glass transition. Meanwhile, geometric motifs known as locally favored structures (LFS) are associated with vitrification in many glassformers. Recent work indicates that the probability of particles found both in locally favored structures (LFS) and excitations decreases significantly upon supercooling suggesting that there is an anti-correlation between them [Ortlieb et al, Nature Commun. 14, 2621 (2023)]. However, the spatial relationship between excitations and LFS remains unclear. By employing state-of-the-art GPU computer simulations and colloid experiments, we analyze this relationship between LFS and excitations in model glassformers. We demonstrate that there is a spatial separation between the two in deeply supercooled liquids. This may be due to the fact that LFS are well-packed, thus they are relatively stable.

cond-mat.soft↗

arXiv2024

Link Node: A Method to Characterize the Chain Topology of Intrinsically Disordered Proteins

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 challenge. Here, we analyze the chain topology of IDPs to characterize their conformations, in combination with molecular dynamics simulation (MD). We systematically compute the Gauss Linking Number ($GLN$) between segments in IDP, and show that the resulting GLN Map can effectively depict an unconventional structure -- physical link, i.e., the entanglement between two segments. The crossing points of physical links are further identified and denoted as Link Nodes. We show that the probability distribution of Link Nodes is highly heterogeneous and there are certain residues that largely affect the chain topology of IDP. Moreover, the structural fluctuations of the vicinity of these residues are largely suppressed, i.e., Link Node provides useful information about the topological constraint imposed on the residues during the conformation fluctuations of IDP. We further reveal that the evolution of the chain topology is considerably slow (with a timescale of hundreds of nanoseconds), which is distinct from the flipping of residue contact.

physics.bio-ph↗