相关论文: Ab initio study of alanine polypeptide chains twis…
We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids - including alternative possible side chain protonation states and their interactions with…
The dynamical response of a tethered semiflexible polymer with self-attractive interactions and subjected to an external force field is numerically investigated by varying stiffness and self-interaction strength. The chain is confined in…
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…
This work describes the development of a third-generation charge optimized many-body (COMB3) potential for Al-C and its application to the investigation of aluminum/graphene nanostructures. In particular, the new COMB3 potential was used to…
The mechanical response of intrinsically disordered proteins (IDPs) and polyampholyte (PA) chains is vital for understanding their biological functions and designing functional materials. We investigate the force-extension behavior of a PA…
The calculation of potential energy surfaces for quantum dynamics can be a time consuming task -- especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
The protein dynamical transition is investigated as a function of protein structure using terahertz time domain spectroscopy (THz-TDS). Measurements performed for native state and denatured hen egg white lysozyme (HEWL) show that protein…
We use the lattice model of directed walks to investigate the conformational as well as the adsorption properties of a semiflexible homopolymer chain immersed in a good solvent in two and three dimensions. To account for the stiffness in…
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art \textit{ab initio} theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete…
The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein…
We have analyzed dynamics on the complex free energy landscape of protein folding in the FOLD-X model, by calculating for each state of the system the mean first passage time to the folded state. The resulting kinetic map of the folding…
Twist-grain-boundary phases in smectics are the geometrical analogs of the Abrikosov flux lattice in superconductors. At large twist angles, the nonlinear elasticity is important in evaluating their energetics. We analytically construct the…
The link between the energy surface of bulk systems and their dynamical properties is generally difficult to establish. Using the activation-relaxation technique (ART nouveau), we follow the change in the barrier distribution of a model of…
Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central…
Phi-values are experimental measures of how the kinetics of protein folding is changed by single-site mutations. Phi-values measure energetic quantities, but are often interpreted in terms of the structures of the transition state ensemble.…
We show that a protein can be trained to recognise multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
Chain molecules play important roles in industry and in living cells. Our focus here is on distinct ways of modeling the stiffness inherent in a chain molecule. We consider three types of stiffnesses -- one yielding an energy penalty for…
Predicting favorable protein-peptide binding events remains a central challenge in biophysics, with continued uncertainty surrounding how nonlocal effects shape the global energy landscape. Here, we introduce peripheral surface information…