相关论文: Dominant Folding Pathways of a WW Domain
The control of ferroelectric domain walls and their dynamics on the nanoscale becomes increasingly important for advanced nanoelectronics and novel computing schemes. One common approach to tackle this challenge is the pinning of walls by…
The rotational damping width \Gamma_{rot} and the compound damping width \Gamma_{comp} are two fundamental quantities that characterize rapidly rotating compound nuclei having finite thermal excitation energy. A two-component structure in…
We devise a novel technique to control the shape of polymer molecular weight distributions (MWDs) in atom transfer radical polymerization (ATRP). This technique makes use of recent advances in both simulation-based, model-free reinforcement…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Collapsin response mediator protein CRMP2 (gene: DPYSL2) is crucial for neuronal development. The homotetrameric CRMP2 complex is regulated via two mechanisms, first by phosphorylation at, and second by reduction and oxidation of the Cys504…
The fascinating high-speed field-driven domain wall (DW) motion along ferrimagnetic nanowires near the angular momentum compensation point (AMCP) is solved based on the generic ferrimagnetic dynamics. The physics of the absences of…
The dynamics of motor protein molecules that have two subunits is investigated using simple discrete stochastic models. Exact steady-state analytical expressions are obtained for velocities and dispersions for any number of intermediate…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
We apply the adaptive time-dependent Density Matrix Renormalization Group method (tDMRG) to the study of transport properties of quantum-dot systems connected to metallic leads. Finite-size effects make the usual tDMRG description of the…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
We study the dynamic structure of lipid domain inclusions embedded within a phase-separated reconstituted lipid bilayer in contact with a swarming flow of gliding filamentous actin. Passive circular domains transition into highly-deformed…
We investigate the dynamics of two interacting diffusing particles in an infinite effectively one dimensional system; the particles interact through a step-like potential of width b and height phi_0 and are allowed to pass one another. By…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
Effective path planning is a pivotal challenge across various domains, from robotics to logistics and beyond. This research is centred on the development and evaluation of the Dynamic Curvature-Constrained Path Planning Algorithm (DCCPPA)…
We construct path integrals for stochastic hybrid reaction-diffusion (RD) processes, in which the reaction terms depend on the discrete state of a randomly switching environment. We proceed by spatially discretizing a given RD system and…
We study the protein folding problem on the base of the quantum approach we proposed recently by considering the model of protein chain with nine amino-acid residues. We introduced the concept of distance space and its projections on a…