Related papers: Automated design of collective variables using sup…

The dynamics of physical systems that require high-dimensional representation can often be captured in a few meaningful degrees of freedom called collective variables (CVs). However, identifying CVs is challenging and constitutes a…

Support vector machines (SVM) and other kernel techniques represent a family of powerful statistical classification methods with high accuracy and broad applicability. Because they use all or a significant portion of the training data,…

Collective variable (CV) or order parameter based enhanced sampling algorithms have achieved great success due to their ability to efficiently explore the rough potential energy landscapes of complex systems. However, the degeneracy of…

Developing an efficient method to accelerate the speed of molecular dynamics is a central theme in the field of molecular simulation. One category among the methods are collective-variable-based methods, which rely on predefined collective…

Training a Support Vector Machine (SVM) requires the solution of a quadratic programming problem (QP) whose computational complexity becomes prohibitively expensive for large scale datasets. Traditional optimization methods cannot be…

The study of the rare transitions that take place between long lived metastable states is a major challenge in molecular dynamics simulations. Many of the methods suggested to address this problem rely on the identification of the slow…

We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…

Automated analyses of the outcome of a simulation have been an important part of atomistic modeling since the early days, addressing the need of linking the behavior of individual atoms and the collective properties that are usually the…

There has been recent interest in the use of machine learning (ML) approaches within mathematical software to make choices that impact on the computing performance without affecting the mathematical correctness of the result. We address the…

Sparse support vector machine (SVM) is a popular classification technique that can simultaneously learn a small set of the most interpretable features and identify the support vectors. It has achieved great successes in many real-world…

Kernelized Support Vector Machines (SVMs) are among the best performing supervised learning methods. But for optimal predictive performance, time-consuming parameter tuning is crucial, which impedes application. To tackle this problem, the…

Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to…

In molecular dynamics simulations, rare events, such as protein folding, are typically studied using enhanced sampling techniques, most of which are based on the definition of a collective variable (CV) along which acceleration occurs.…

The determination of efficient collective variables is crucial to the success of many enhanced sampling methods. As inspired by previous discrimination approaches, we first collect a set of data from the different metastable basins. The…

Chemical compound space (CCS), the set of all theoretically conceivable combinations of chemical elements and (meta-)stable geometries that make up matter, is colossal. The first principles based virtual sampling of this space, for example…

High-dimensional complex systems can be studied through multivariate analysis, as Principal Component Analysis, however large samples of observations frequently are needed for it. Here it is examined a method for small samples based on…

Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…

Monte Carlo simulations are widely used to simulate complex molecular systems, but standard approaches suffer from metastability. Lately, the use of non-local proposal updates in a collective-variable (CV) space has been proposed in several…

A popular way to accelerate the sampling of rare events in molecular dynamics simulations is to introduce a potential that increases the fluctuations of selected collective variables. For this strategy to be successful, it is critical to…

Support vector machine (SVM) is a particularly powerful and flexible supervised learning model that analyzes data for both classification and regression, whose usual algorithm complexity scales polynomially with the dimension of data space…