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Thermal spike model (TSM) is presently a widely accepted mechanism of swift heavy ion (SHI) - matter interaction. It provides explanation to various SHI induced effects including mixing across interfaces. The model involves electron-phonon…
Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs…
The emerging field of stochastic thermodynamics extends classical ideas of entropy, heat and work to non-equilibrium systems. One notable finding is that the second law of thermodynamics typically only holds after taking appropriate…
The entanglement entropy encodes fundamental characteristics of quantum many-body systems, and is particularly subtle in non-Hermitian settings where eigenstates generically become non-orthogonal. In this work, we find that negative…
Inverse design has made vast physical parameter spaces a substrate for emergent behavior. In sensing, the stakes of this principle are sharpest at the analog-to-digital boundary, where any information the hardware fails to capture is…
Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
Recently, some of us developed a novel model glass-forming liquid with k extra interactions with pseudo neighbours to each liquid particle over and above the regular interactions with its neighbours. Analysis of the structure and dynamics…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
We review recent results on the potential energy landscape (PES) of model liquids. The role of saddle-points in the PES in connecting dynamics to statics is investigated, confirming that a change between minima-dominated and…
Distinct entropy definitions have been used to obtain an inverse correlation between the residual size and entropy for Heavy Ion Collisions. This explains the existence of several temperatures for different residual size bins, as reported…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively…
Aromatic $\pi$-stacking interactions play an important role in both natural and artificial systems, influencing processes such as charge separation in photosynthesis and charge transport in organic semiconductors. Controlling the geometry…
We report on microscopic tight-binding modeling of surface states in Bi$_2$Se$_3$ three-dimensional topological insulator, based on a sp$^3$ Slater-Koster Hamiltonian, with parameters calculated from density functional theory. The effect of…
Higher-order topological insulators (HOTIs) are systems with topologically protected in-gap boundary states localized at their $(d-n)$-dimensional boundaries, with $d$ the system dimension and $n$ the order of the topology. This work…
Non-Hermiticity from non-reciprocal hoppings has been shown recently to demonstrate the non-Hermitian skin effect (NHSE) under open boundary conditions (OBCs). Here we study the interplay of this effect and the Anderson localization in a…
We present the results of theoretical study of surface state properties in a two-dimensional model for triplet $p$-wave superconductors. We derive boundary conditions for Eilenberger equations at rough interfaces and develop the approach…
Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve description of IDPs/IDRs, but are largely in disagreement with solution…
Black silicon (BSi) is a synthetic nanomaterial with high aspect ratio nano protrusions inducing several interesting properties such as a very large absorptivity of incident radiation. We have recently shown that heavily doping the BSi in…
A quantitative model of the mobility of functionalized particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles anchored through…