Related papers: Predicting the orientation of adsorbed proteins st…

The possibility to control electrokinetic transport through carbon and hexagonal boron nitride (hBN) nanotubes has recently opened new avenues for nanofluidic approaches to face outstanding challenges such as energy production and…

The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…

The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…

In this paper, we introduce an approach to the protein folding problem from the point of view of statistical physics. Protein folding is a stochastic process by which a polypeptide folds into its characteristic and functional 3D structure…

We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…

We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…

Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics…

When a chromophore interacts with titrable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH…

Anisotropic particles oriented in a specific direction can act as artificial atoms and molecules, and their controlled assembly can result in a wide variety of ordered structures. Towards this, we demonstrate the orientation transitions of…

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…

Molecular dynamics simulations have been used extensively to determine equilibrium properties of the electrode-electrolyte interface in supercapacitors held at various potentials. While such studies are essential to understand and optimize…

Computational screening for new and improved catalyst materials relies on accurate and low-cost predictions of key parameters such as adsorption energies. Here, we use recently developed compressed sensing methods to identify descriptors…

The time-dependent, mean-field Newns-Anderson model for a spin-polarised adsorbate approaching a metallic surface is solved in the wide-band limit. Equations for the time-evolution of the electronic structure of the adsorbate-metal system…

Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…

We present a position Langevin equation for overdamped particle motion on rough two-dimensional surfaces. A Brownian Dynamics algorithm is suggested to evolve this equation numerically, allowing for the prediction of effective (projected)…

Precise control and study of molecules is challenging due to the variety of internal degrees of freedom and local coordinates that are typically not controlled in an experiment. Employing quantum gas microscopy to position and resolve the…

In this thesis we study the lateral electrostatic interaction between a pair of non-identical, moderately charged colloidal particles trapped at an electrolyte interface in the limit of short inter-particle separations. Using a simplified…

Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. Here we develop a workflow…

We implement a well-established concept to consider dispersion effects within a Poisson-Boltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters…

We propose a self-consistent model taking into account variations in adsorption properties of the adsorbent surface in the process of adsorption--desorption of molecules of gas on it. We introduce a dimensionless coupling parameter that…