Related papers: Enhanced sampling and applications in protein fold…
We present a model for the efficient simulation of generic bilayer membranes. Individual lipids are represented by one head- and two tail-beads. By means of simple pair potentials these robustly self-assemble to a fluid bilayer state over a…
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…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
We report 10 successfully folding events of trpzip2 by molecular dynamics simulation. It is found that the trizip2 can fold into its native state through different zipper pathways, depending on the ways of forming hydrophobic core. We also…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
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…
Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single…
Simulated and parallel tempering are families of Markov Chain Monte Carlo algorithms where a temperature parameter is varied during the simulation to overcome bottlenecks to convergence due to multimodality. In this work we introduce and…
This article demonstrates that flexible and statistically tractable multi-modal diffusion models can be attained by transformation of simple well-known diffusion models such as the Ornstein-Uhlenbeck model, or more generally a Pearson…
Jamming is a common feature of out of equilibrium systems showing slow relaxation dynamics. Here we review our efforts in understanding jamming in granular materials using experiments and computer simulations. We first obtain an estimation…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
In this paper, we present a theoretical simulation of 87Rb absorption spectrum in a thermal cm-cell which is adaptive to the experimental observation. In experiment, the coupling and probe beams are configured to copropagate but…
Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…
Folding of the triangular lattice in a discrete three-dimensional space is investigated numerically. Such ``discrete folding'' has come under through theoretical investigation, since Bowick and co-worker introduced it as a simplified model…