Dataset Information

Identification of kinetic order parameters for non-equilibrium dynamics.

ABSTRACT: A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly varying collective variables, where subsequent analyses are made, such as clustering or estimation of free energy profiles or Markov state models. However, existing "dynamical" dimension reduction methods, such as the time-lagged independent component analysis (TICA), are only valid if the dynamics obeys detailed balance (microscopic reversibility) and typically require long, equilibrated simulation trajectories. Here, we develop a dimension reduction method for non-equilibrium dynamics based on the recently developed Variational Approach for Markov Processes (VAMP) by Wu and Noé. VAMP is illustrated by obtaining a low-dimensional description of a single file ion diffusion model and by identifying long-lived states from molecular dynamics simulations of the KcsA channel protein in an external electrochemical potential. This analysis provides detailed insights into the coupling of conformational dynamics, the configuration of the selectivity filter, and the conductance of the channel. We recommend VAMP as a replacement for the less general TICA method.

SUBMITTER: Paul F

PROVIDER: S-EPMC6486394 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Identification of kinetic order parameters for non-equilibrium dynamics.

Paul Fabian F Wu Hao H Vossel Maximilian M de Groot Bert L BL Noé Frank F

The Journal of chemical physics 20190401 16

A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly varying collective variables, where subsequent analyses are made, such as clustering or estimation of free energy profiles or Markov state models. However, existing "dynamical" dimension reduction methods, such as the time-lagged independent component analysis (TICA), are only valid if the dynamics obeys detailed balance (microscopic reve ...[more]

PMID: 31042914

Similar Datasets

Project description:The use of solar photovoltaic systems (PVs) is increasing as a clean and affordable source of electric energy. The Pv cell is the main component of the PV system. To improve the performance, control, and evaluation of the PV system, it is necessary to provide accurate design and to define the intrinsic parameters of the solar cells. There are many methods for optimizing the parameters of the solar cells. The first class of methods is called the analytical methods that provide the model parameters using datasheet information or I-V curve data. The second class of methods is the optimization-based methods that define the problem as an optimization problem. The optimization problem objective is to minimize the error metrics and it is solved using metaheuristic optimization algorithms. The third class of methods is composed of a hybrid of both the analytical and the metaheuristic approaches, some parameters are computed by the analytical approach and the rest are found using metaheuristic optimization algorithms. Research in this area faces two challenges; (1) finding an optimal model for the parameters of the solar cells and (2) the lack of data about the photovoltaic cells. This paper proposes an optimization-based algorithm for accurately estimating the parameters of solar cells. It is using the Improved Equilibrium Optimizer algorithm (IEO). This algorithm is improved using the Opposition Based Learning (OBL) at the initialization phase of EO to improve its population diversity in the search space. Opposition-based Learning (OBL) is a new concept in machine learning inspired by the opposite relationship among entities. There are two common models for solar cells; the single diode model (SDM) and double diode model (DDM) have been used to demonstrate the capabilities of IEO in estimating the parameters of solar cells. The proposed methodology can find accurate solutions while reducing the computational cost. Compared to other existing techniques, the proposed algorithm yields less mean absolute error. The results were compared with seven optimization algorithms using data of different solar cells and PV panels. The experimental results revealed that IEO is superior to the most competitive algorithms in terms of the accuracy of the final solutions.

Project description:BackgroundWe consider a focal adhesion to be made up of molecular complexes, each consisting of a ligand, an integrin molecule, and associated plaque proteins. Free energy changes drive the binding and unbinding of these complexes and thereby controls the focal adhesion's dynamic modes of growth, treadmilling and resorption.Principal findingsWe have identified a competition among four thermodynamic driving forces for focal adhesion dynamics: (i) the work done during the addition of a single molecular complex of a certain size, (ii) the chemical free energy change associated with the addition of a molecular complex, (iii) the elastic free energy change associated with deformation of focal adhesions and the cell membrane, and (iv) the work done on a molecular conformational change. We have developed a theoretical treatment of focal adhesion dynamics as a nonlinear rate process governed by a classical kinetic model. We also express the rates as being driven by out-of-equilibrium thermodynamic driving forces, and modulated by kinetics. The mechanisms governed by the above four effects allow focal adhesions to exhibit a rich variety of behavior without the need to introduce special constitutive assumptions for their response. For the reaction-limited case growth, treadmilling and resorption are all predicted by a very simple chemo-mechanical model. Treadmilling requires symmetry breaking between the ends of the focal adhesion, and is achieved by driving force (i) above. In contrast, depending on its numerical value (ii) causes symmetric growth, resorption or is neutral, (iii) causes symmetric resorption, and (iv) causes symmetric growth. These findings hold for a range of conditions: temporally-constant force or stress, and for spatially-uniform and non-uniform stress distribution over the FA. The symmetric growth mode dominates for temporally-constant stress, with a reduced treadmilling regime.SignificanceIn addition to explaining focal adhesion dynamics, this treatment can be coupled with models of cytoskeleton dynamics and contribute to the understanding of cell motility.

Dataset Information

Identification of kinetic order parameters for non-equilibrium dynamics.

Publications

Identification of kinetic order parameters for non-equilibrium dynamics.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets