Related papers: Soliton mediated protein folding
Soliton dynamics in a large variety of longitudinally modulated lattices are studied in terms of phase space analysis for an effective particle approach and direct numerical simulations. Complex soliton dynamics are shown to depend strongly…
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…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
We propose a solitonic dynamical system over finite fields that may be regarded as an analogue of the box-ball systems. The one-soliton solutions of the system, which have nested structures similar to fractals, are also proved. The…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
Interaction of Double sine-Gordon solitons with a space dependent potential wall and also a potential well has been investigated by employing an analytical model based on the collective coordinate approach. The potential has been added to…
A novel, protean, topological soliton has recently been shown to emerge in systems of repulsive particles in cylindrical geometries, whose statics is described by the number-theoretical objects of phyllotaxis. Here we present a minimal and…
Solitons in general are configurations of extended fields which move like isolated particles. Vector bright solitons can occur in a two-component self-attractive Bose-Einstein condensate. If the components of the condensate have different…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
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…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
Ultracold condensates provide a unique platform for exploring soliton physics. Motivated by the recent experiments realizing the sine-Gordon model in a split one-dimensional (1D) BEC, we demonstrate that this system naturally supports…
It's been said that "mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better". Here we aim for something even better. We try to combine mathematical physics and biology into a picoscope of…
Various soliton-obstruction systems have been studied from analytical perspective. We have used collective coordinate to approach the dynamics of solitons as they meet a potential obstruction in a form of square barriers and holes for three…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…