Related papers: Simultaneous identification of multiple binding si…
We consider a family of percolation models in which geometry and connectivity are defined by two independent random processes. Such models merge characteristics of discrete and continuous percolation. We develop an algorithm allowing…
We study a simple model of interacting bosons on a d-dimensional cubic lattice whose dynamics conserves both total boson number and total boson dipole moment. This model provides a simple framework in which several remarkable consequences…
Many-body localization for a system of bosons trapped in a one dimensional lattice is discussed. Two models that may be realized for cold atoms in optical lattices are considered. The model with a random on-site potential is compared with…
The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density…
The nonlinear Poisson-Boltzmann equation (NPBE) is an elliptic partial differential equation used in applications such as protein interactions and biophysical chemistry (among many others). It describes the nonlinear electrostatic potential…
Multi-component fluid flow simulations in multi-scale porous structures often involve regions that are under-resolved at practical computational resolutions. Accurately capturing the contributions from these unresolved regions is critical.…
Proteins inherently possess a consistent sequence-structure duality. The abundance of protein sequence data, which can be readily represented as discrete tokens, has driven fruitful developments in protein language models (pLMs). A key…
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)…
We present the detailed analysis of the diffusive transport of spatially inhomogeneous fluid mixtures and the interplay between structural and dynamical properties varying on the atomic scale. The present treatment is based on different…
We investigate the aggregation of amphiphilic molecules by adapting the two-state Muller-Lee-Graziano model for water, in which a solvent-induced hydrophobic interaction is included implicitly. We study the formation of various types of…
Cells use homeostatic mechanisms to maintain an optimal composition of distinct types of phospholipids in cellular membranes. The hydrophilic dipolar layer at the membrane interface, composed of phospholipid headgroups, regulates the…
Thermodynamic properties of charge-stabilised colloidal suspensions are commonly modeled by implementing the mean-field Poisson-Boltzmann (PB) theory within a cell model. This approach models a bulk system by a single macroion, together…
The dielectric properties of proteins, particularly in their hydrated state, have been extensively studied. Numerous theoretical and experimental investigations have reported values of both the permittivity and the intrinsic dipole moments…
Among an infinite number of possible folds, nature has chosen only about 1000 distinct folds to form protein structures. Theoretical studies suggest that selected folds are intrinsically more designable than others; these selected folds are…
As a common view the hydrophobic association between molecular-scale binding partners is supposed to be dominantly driven by entropy. Recent calorimetric experiments and computer simulations heavily challenge this established paradigm by…
Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…
Models of relativistic heavy ion collisions typically involve both a hydrodynamic module to describe the high density liquid-like phase and a Boltzmann module to simulate the low density break-up phase which is gas-like. Coupling the…
In this work we discuss the coupling of two mesoscopic approaches for fluid dynamics, namely the lattice Boltzmann method (LB) and the multiparticle collision dynamics (MPCD) \cite{kapral2008multiparticle} to design a new class of flexible…
We use a coarse-grained model to study the conformational changes in two barley proteins, LTP1 and its ligand adduct isoform LTP1b, that result from their adsorption to the air-water interface. The model introduces the interface through…
This work investigates the out-of-equilibrium dynamics of dipole and higher-moment conserving systems with long-range interactions, drawing inspiration from trapped ion experiments in strongly tilted potentials. We introduce a hierarchical…