Related papers: Molecular Dynamics-Based Strength Estimates of Bet…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
Soft robots have immense potential given their inherent safety and adaptability, but challenges in soft actuator forces and design constraints have limited scaling up soft robots to larger sizes. Electrothermal shape memory alloy (SMA)…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
Proteinoids are solidified gels made from poly(amino acids) based polymers that exhibit oscillatory electrical activity. It has been proposed that proteinoids are capable of performing analog computing as their electrical activity can be…
We present new ab initio calculations of the electronic structure of various atoms and molecules in strong magnetic fields ranging from B=10^12 G to 2x10^15 G, appropriate for radio pulsars and magnetars. For these field strengths, the…
We present a proof of concept that machine learning techniques can be used to predict the properties of CNOHF energetic molecules from their molecular structures. We focus on a small but diverse dataset consisting of 109 molecular…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
For several decades, experimental and computational studies have been used to investigate the potential functional role of knots in protein structures. A property that has attracted considerable attention is thermal stability, i.e., the…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
Crystal dislocation dynamics, especially at high temperatures, represents a subject where experimental phenomenological input is commonly required, and parameter-free predictions, starting from quantum methods, have been beyond reach. This…
Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport,…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We introduce a new measure of the structure of a liquid which is the softness of the mean-field potential developed by us earlier. We find that this softness is sensitive to small changes in the structure. We then study its correlation with…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
Motivation: Site directed mutagenesis is widely used to understand the structure and function of biomolecules. Computational prediction of protein mutation impacts offers a fast, economical and potentially accurate alternative to laboratory…
The statistical properties of protein folding within the {\phi}^4 model are investigated. The calculation is performed using statistical mechanics and path integral method. In particular, the evolution of heat capacity in term of…
In a recent Letter, Gutin, Abkevich, and Shakhnovich (GAS) reported on a series of dynamical Monte Carlo simulations on lattice models of proteins. Based on these highly simplified models, they found that four different potential energies…