Related papers: Rethinking hydrogen-bond kinetics
Thermodynamics, introduced over two centuries ago, remains foundational to our understanding of physical, chemical, biological, and engineering systems. Its principles are traditionally grounded in the statistical mechanics framework, which…
In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase…
The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a…
Motivated by recent simulations and by experiments on aggregation of gliding bacteria, we study a model of the collective dynamics of self-propelled hard rods on a substrate in two dimensions. The rods have finite size, interact via…
Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. Here we employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total…
We introduce and study a new class of kinetic equations, which arise in the description of nonequilibrium macroscopic dynamics of soliton gases with elastic collisions between solitons. These equations represent nonlinear…
Halogen bonding has emerged as an important noncovalent interaction in a myriad of applications, including drug design, supramolecular assembly, and catalysis. Current understanding of the halogen bond is informed by electronic structure…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Liquid water is reluctant to lose hydrogen-bond coordination. Here we reveal that it also demands contraction and reorientation of the second molecular shell to compensate for coordination defects. Such molecular principle will be shown to…
The basis for a hydrodynamic description of granular gases is discussed for a low density gas of smooth, inelastic hard spheres. The more fundamental mesoscopic description is taken to be the nonlinear Boltzmann kinetic equation. Two…
In the quest to understand large-scale collective behavior in active matter, the complexity of hydrodynamic and phoretic interactions remains a fundamental challenge. To date, most works either focus on minimal models that do not (fully)…
Equations of state for hydrogen bonding fluids are typically described by two energy scales. A short range highly directional hydrogen bond energy scale, as well as a reference energy scale which accounts for dispersion and orientationally…
We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…
The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs)…
The peculiar structuring of liquid water stems from a fine-tuned molecular principle embodying the two different interaction demands of the water molecule: The formation of hydrogen bonds or the compensation for coordination defects. Here…
Water, a subject of human fascination for millennia, is likely the most studied substance on Earth, with an entire scientific field -- hydrodynamics -- dedicated to understanding water in motion. However, when water flows through…
We develop an approach to liquid thermodynamics based on collective modes. We perform extensive molecular dynamics simulations of noble, molecular and metallic liquids and provide the direct evidence that liquid energy and specific heat are…
Water is an associated liquid in which the main intermolecular interaction is the hydrogen bond (HB) which is limited to four per atom, independently of the number of neighbours. We have considered a hydrogen bond net superposed on Bernal's…
The {\em hydrodynamic} approach to a continuum mechanical description of granular behavior is reviewed and elucidated. By considering energy and momentum conservation simultaneously, the general formalism of {\em hydrodynamics} provides a…
The local structure of liquid water as a function of temperature is a source of intense research. This structure is intimately linked to the dynamics of water molecules, which can be measured using Raman and infrared spectroscopies. The…