相关论文: Multi-Overlap Simulations for Transitions between …

We propose a method for efficient simulations in extended ensembles, useful, e.g., for the study of problems with complex energy landscapes and for free energy calculations. The main difficulty in such simulations is the estimation of the a…

Excited states exhibiting double excitation character are notoriously difficult to model using conventional single-reference methods, such as adiabatic time-dependent density-functional theory (TD-DFT) or equation-of-motion coupled cluster…

We study the free energy landscape of the small peptide Met-enkephalin. Our data were obtained from a generalized-ensemble Monte Carlo simulation taking the interactions among all atoms into account. We show that the free energy landscape…

We introduce and analyze free energy landscapes defined by associating to any point inside the sphere a free energy calculated on a thin spherical band around it, using many orthogonal replicas. This allows us to reinterpret, rigorously…

We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…

Experience replay \citep{lin1993reinforcement, mnih2015human} is a widely used technique to achieve efficient use of data and improved performance in RL algorithms. In experience replay, past transitions are stored in a memory buffer and…

We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…

Imbalances in covariates between treatment groups are frequent in observational studies and can lead to biased comparisons. Various adjustment methods can be employed to correct these biases in the context of multi-level treatments ($>$ 2).…

Although machine-learning potentials have recently had substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio…

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…

In this paper, we revisit the regret of undiscounted reinforcement learning in MDPs with a birth and death structure. Specifically, we consider a controlled queue with impatient jobs and the main objective is to optimize a trade-off between…

The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in…

A system of neutral atoms trapped in an optical lattice and dispersively coupled to the field of an optical cavity can realize a variation of the Bose-Hubbard model with infinite-range interactions. This model exhibits a first order quantum…

In this paper we accomplish the development of the fast rank-adaptive solver for tensor-structured symmetric positive definite linear systems in higher dimensions. In [arXiv:1301.6068] this problem is approached by alternating minimization…

In the paradigm of multi-task learning, mul- tiple related prediction tasks are learned jointly, sharing information across the tasks. We propose a framework for multi-task learn- ing that enables one to selectively share the information…

The wrapping equilibria of one and two adsorbing cylinders are studied along a semi-flexible filament (polymer) due to the interplay between elastic rigidity and short-range adhesive energy between the cylinder and the filament. We show…

Finding collective variables to describe some important coarse-grained information on physical systems, in particular metastable states, remains a key issue in molecular dynamics. Recently, machine learning techniques have been intensively…

Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant…

Relaxation phenomena in glasses can be related to jump processes between different minima of the potential energy in the configuration space. These transitions play a key role in the low temperature regime, giving rise to tunneling systems…