Related papers: How does the first water shell fold proteins so fa…
Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…
We study theoretically the thermodynamics, over a broad temperature range (5 C to 125 C), related to hydrated water upon protein unfolding. The hydration effect is modeled as interacting dipoles in an external field, mimicking the influence…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
Different hypotheses have been proposed to explain the mechanism for the extremely low friction coefficient of carbon coatings and its undesired dependence on air humidity. A decisive atomistic insight is still lacking because of the…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
When an ice crystal is born from liquid water two key changes occur: (i) the molecules order; and (ii) the mobility of the molecules drops as they adopt their lattice positions. Most research on ice nucleation (and crystallization in…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
Experiments in bulk water confirm the existence of two local arrangements of water molecules with different densities, but, because of inevitable freezing at low temperature $T$, can not ascertain whether the two arrangements separate in…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
Glasses and gels are the two dynamically arrested, disordered states of matter. Despite their importance, their similarities and differences remain elusive, especially at high density. We identify dynamical and structural signatures which…
Structuring wheat gluten proteins into gels with tunable mechanical properties would provide more versatility for the production of plant protein-rich food products. Gluten, a strongly elastic protein material insoluble in water, is hardly…
We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We obtain…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
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…
In this study, the additional heat capacity which appear during the water dissociation of the proteins that are one of the soft materials, have been considered by the statistical mechanical methods. For this purpose, taking the electric…
While deeply supercooled liquids exhibit divergent viscosity and increasingly heterogeneous dynamics as the temperature drops, their structure shows only seemingly marginal changes. Understanding the nature of relaxation processes in this…