Related papers: Random-phase-approximation theory for sequence-dep…
Polyampholyte field theory and explicit-chain molecular dynamics models of sequence-specific phase separation of a system with two intrinsically disordered protein (IDP) species indicate consistently that a substantial polymer excluded…
The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…
In reaction path optimization, such as the calculation of a minimum energy path (MEP) between given reactant and product configurations of atoms, it is advantageous to start with an initial guess where close proximity of atoms is avoided…
This Ph.D. thesis derives the equations of the Faddeev Random Phase Approximation (FRPA) and applies the method to a set of small atoms and molecules. The occurence of RPA instabilities in the dissociation limit is addressed in molecules…
We study the vapour-liquid phase behaviour of an ionic fluid confined in a random porous matrix formed by uncharged hard sphere particles. The ionic fluid is modelled as an equimolar binary mixture of oppositely charged equisized hard…
The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this…
Proteins and nucleic acids can spontaneously self-assemble into membraneless droplet-like compartments, both in vitro and in vivo. A key component of these droplets are multi-valent proteins that possess several adhesive domains with…
Biomolecular condensates composed of intrinsically disordered proteins (IDPs) are vital for proper cellular function, and their dysfunction is associated with diseases including neurodegeneration and cancer. Despite their biological…
The time-dependent density functional theory (TDDFT) provides a unified description of the structure and reaction. The linear approximation leads to the random-phase approximation (RPA) which is capable of describing a variety of collective…
We present an efficient implementation of the random phase approximation (RPA) for molecular systems within the domain-based local pair natural orbital (DLPNO) framework. With optimized parameters, DLPNO-RPA achieves approximately 99.9%…
Motility-induced phase separation (MIPS) is a well-studied nonequilibrium collective phenomenon observed in active particles. Recently, there has been growing interest in how coupling the self-propulsion of active particles to chemical…
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…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular…
We outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein…
The human proteome is enriched in proteins that do not fold into a stable 3D structure. These intrinsically disordered proteins (IDPs) spontaneously fluctuate between a large number of configurations in their native form. Remarkably, the…
The adiabatic connection fluctuation-dissipation theorem with the random phase approximation (RPA) has recently been applied with success to obtain correlation energies of a variety of chemical and solid state systems. The main merit of…
The accurate computation of non-linear optical properties (NLOPs) in large polymers requires accounting for electronic correlation effects with a reasonable computational cost. The Random Phase Approximation (RPA) used in the adiabatic…
Isotachophoresis (ITP) is a versatile electrophoretic technique which can be used for sample preconcentration, separation, purification, mixing, and control and acceleration of chemical reactions. Although the basic technique is nearly a…
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…