Related papers: Finding dominant transition pathways via global op…

Efficient algorithms for the calculation of minimum energy paths of magnetic transitions are implemented within the geodesic nudged elastic band (GNEB) approach. While an objective function is not available for GNEB and a traditional line…

We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with…

Efficient analysis and simulation of multiscale stochastic systems of chemical kinetics is an ongoing area for research, and is the source of many theoretical and computational challenges. In this paper, we present a significant improvement…

Adaptive traffic signal control (ATSC) can effectively reduce vehicle travel times by dynamically adjusting signal timings but poses a critical challenge in real-world scenarios due to the complexity of real-time decision-making in dynamic…

Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial…

We apply a set of machine-learning (ML) techniques for the global exploration of the phase diagrams of two frustrated 2D Ising models with competing interactions. Based on raw Monte Carlo spin configurations generated for random system…

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…

Computing accurate rate constants for catalytic events occurring at the surface of a given material represents a challenging task with multiple potential applications in chemistry. To address this question, we propose an approach based on a…

In this work, we present a transition-state optimization protocol based on the Mode-Tracking algorithm [J. Chem. Phys. 118 (2003) 1634]. By calculating only the eigenvector of interest instead of diagonalizing the full Hessian matrix and…

This paper discusses the adaptive sampling problem in a nonholonomic mobile robotic sensor network for efficiently monitoring a spatial field. It is proposed to employ Gaussian process to model a spatial phenomenon and predict it at…

Cellular Automata (CAs) are computational models that can capture the essential features of systems in which global behavior emerges from the collective effect of simple components, which interact locally. During the last decades, CAs have…

Active Learning aims to optimize performance while minimizing annotation costs by selecting the most informative samples from an unlabelled pool. Traditional uncertainty sampling often leads to sampling bias by choosing similar uncertain…

In this paper, we have developed an approach to generate test data for path coverage based testing. The main challenge of this kind testing lies in its ability to build efficiently such a test suite in order to minimize the number of…

We show that molecular dynamics based moves in the Minima Hopping (MH) method are more efficient than saddle point crossing moves which select the lowest possible saddle point. For binary systems we incorporate identity exchange moves in a…

We present an efficient sampling method for computing a partition function and accelerating configuration sampling. The method performs a random walk in the $\lambda$ space, with $\lambda$ being any thermodynamic variable that characterizes…

We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…

Path smoothness is often overlooked in path imitation learning from expert demonstrations. In this paper, we introduce a novel learning method, termed deep angular A* (DAA*), by incorporating the proposed path angular freedom (PAF) into A*…

Autonomous driving vehicles aim to free the hands of vehicle operators, helping them to drive easier and faster, meanwhile, improving the safety of driving on the highway or in complex scenarios. Automated driving systems (ADS) are…

Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the…

We use the Dominant Reaction Pathway (DRP) approach to study the dynamics of the folding of a beta-hairpin, within a model which accounts for both native and non-native interactions. We compare the most probable folding pathways calculated…