Residue Folding Degree—Relationship to Secondary Structure Categories and Use as Collective Variable

Recently, we have shown that the residue folding degree, a network-based measure of folded content in proteins, is able to capture backbone conformational transitions related to the formation of secondary structures in molecular dynamics (MD) simulations. In this work, we focus primarily on developing a collective variable (CV) for MD based on this residue-bound parameter to be able to trace the evolution of secondary structure in segments of the protein. We show that this CV can do just that and that the related energy profiles (potentials of mean force, PMF) and transition barriers are comparable to those found by others for particular events in the folding process of the model mini protein Trp-cage. Hence, we conclude that the relative segment folding degree (the newly proposed CV) is a computationally viable option to gain insight into the formation of secondary structures in protein dynamics. We also show that this CV can be directly used as a measure of the amount of α-helical content in a selected segment.

Optical solitons for the Kaup–Newell equation by collective variables method

In this work, we present a collective variable (CV) approach to establish dispersive solitary wave solutions for the Kaup–Newell Equation (KNE). The full CV theory has been utilized to enunciate the soliton molecules through its ground-laying parameters including the power of each pulse, phase and center-of-mass. Additionally, the dynamics of an ultra short pulse has been analyzed by using CV. This work may be utilized for various dynamics of solitons as well as the influence the amplitude, temporal position, frequency, phase and chirp on the solitons’ nonlinear parameters. Moreover, the numerical simulations have been designed by means of appropriate parameter values to explain more on the obtained results.

Novel Optical Solitons to the Perturbed Gerdjikov-Ivanov Equation Via Collective Variables

The objective of this research is to study the collective variable (CV) technique to explore an important form of Schrödinger equation known as the Gerdjikov-Ivanov (GI) equation which expresses the dynamics of solitons for optical fibers in terms of pulse parameters. These parameters are temporal position, amplitude, width, chirp, phase, and frequency known as collective variables (CVs). This is an effective and dynamic mathematical gadget to obtain soliton solutions of non-dimensional as well as perturbed GI equations. Moreover, an established numerical scheme that is the fourth-order Runge-Kutta method is exerted for the numerical simulation of the revealing coupled system of six ordinary differential equations which represent all the CVs included in the pulse ansatz. The CV approach is used to determine the evolution of pulse parameters with the propagation distance and illustrated it illustrated it graphically. Furthermore, Figures show the compelling periodic oscillations of pulse chirp, width, frequency and amplitude of soliton. For various values of super-Gaussian pulse parameters, the numerical behavior of solitons to illustrate variations in CVs is provided. Other significant aspects with regards to the current investigation are also inferred.

Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Framework

We have formulated a Riemannian framework for describing the geometry of collective variable spaces of biomolecules within the context of molecular dynamics (MD) simulations. The formalism provides a theoretical framework to develop enhanced sampling techniques, path-finding algorithms, and transition rate estimators consistent with a Riemannian treatment of the collective variable space, where the quantities of interest such as the potential of mean force (PMF) and minimum free energy path (MFEP) remain invariant under coordinate transformation. Specific algorithms within this framework are discussed such as the Riemannian umbrella sampling, the Riemannian string method, and a Riemannian-Bayesian estimator of free energy and diffusion constant, which can be used to estimate the transition rate along an MFEP.

Optical solitons via the collective variable method for the classical and perturbed Chen–Lee–Liu equations

In this article, the collective variable method to study two types of the Chen–Lee–Liu (CLL) equations, is employed. The CLL equation, which is also the second member of the derivative nonlinear Schrödinger equations, is known to have vast applications in optical fibers, in particular. More specifically, a consideration to the classical Chen–Lee–Liu (CCLL) and the perturbed Chen–Lee–Liu (PCLL) equations, is made. Certain graphical illustrations of the simulated numerical results that depict the pulse interactions in terms of the soliton parameters are provided. Also, the influential parameters in each model that characterize the evolution of pulse propagation in the media, are identified.