Related papers: Multi-scale approach for self-Assembly and protein…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
Hydrophobic hydration plays a crucial role in self-assembly processes over multiple length-scales, but the extrapolation of molecular-scale models to larger length-scale hydration phenomena is sometimes not warranted. Scaled-particle…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Self-assembly of nanoparticles is an important tool in nanotechnology, with numerous applications including thin films, electronics, and drug delivery. We study the deposition of ionic nanoparticles on a glass substrate both experimentally…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
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…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
In this work we examine the nucleation from NaCl aqueous solutions within nano-confined environments, employing enhanced sampling molecular dynamics simulations integrated with machine learning-derived reaction coordinates. Through our…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Liquids under confinement differ in behavior from their bulk counterparts and can acquire properties that are specific to the confined phase and linked to the nature and structure of the host matrix. While confined liquid water is not a new…
Partitioning and transport of water and small solutes into and through nanopores is important to a variety of chemical and biological processes and applications. Here we study the partitioning of positive ions of increasing size into the…
Using molecular dynamics simulations, we reveal emergent properties of hydrated electrode interfaces that while molecular in origin are integral to the behavior of the system across long times scales and large length scales. Specifically,…