相关论文: Cold and Warm Denaturation of Proteins

Water desalination through nanopores has been shown to be a promising alternative to the currently water purification processes. In spite the results in this direction obtained by means of computational simulations were animating there are…

We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…

We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem…

Water molecules and molecular chaperones efficiently help the protein folding process. Here we describe their action in the context of the energy and topological networks of proteins. In energy terms water and chaperones were suggested to…

We use molecular dynamics simulations in two dimensions to investigate the possibility that a core-softened potential can reproduce static and dynamic anomalies found experimentally in liquid water: (i) the increase in specific volume upon…

We present a new model of warm dense matter that represents an intermediate approach between the relative simplicity of ''one-ion'' average atom models and the more realistic but computationally expensive ab initio simulation methods.…

In this work, we study a protein synthesis degradation process by defining a general mathematical model. Using generating function technique we present a method that allows exact calculation of joint probability distribution of protein…

Photoactive proteins absorb light and undergo structural changes that enable them to perform essential biological functions. These proteins are critical for understanding light-induced biological processes, making them important in…

The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…

A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of gaining insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation…

The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…

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…

A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal…

Methanol-water liquid mixtures have been investigated by high-energy synchrotron X-ray and neutron diffraction at low temperatures. We are thus able to report the first complete sets of both X-ray and neutron weighted total scattering…

Activated processes such as protein unfolding are highly sensitive to heterogeneity in the environment. We study a highly simplified model of a protein in a random heterogeneous environment, a model of the in vivo environment. It is found…

Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…

The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…

The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…

We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…

Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…