相关论文: A perturbative solution to metadynamics ordinary d…
Uncovering the underlying causal mechanisms of complex real-world systems remains a significant challenge, as these systems often entail high data collection costs and involve unknown interventions. We introduce MetaCaDI, the first…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to…
By drawing a parallel between metadynamics and self interacting models for polymers, we study the longtime convergence of the original metadynamics algorithm in the adiabatic setting, namely when the dynamics along the collective variables…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
We present a general framework to study the metastability of random perturbations of dynamical systems. It integrates techniques from the theory of Markov processes, in particular the resolvent approach to metastability, with the spectral…
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective…
Dynamical systems studies of differential equations often focus on the behavior of solutions near critical points and on invariant manifolds, to elucidate the organization of the associated flow. In addition, effective methods, such as the…
The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
Synthesis remains a challenge for advancing materials science. A key focus of this challenge is how to enable selective synthesis, particularly as it pertains to metastable materials. This perspective addresses the question: how can…
We consider a novel model of stochastic replicator dynamics for potential games that converts to a Langevin equation on a sphere after a change of variables. This is distinct from the models studied earlier. In particular, it is ill-posed…
As a two-dimensional planar material with low depth profile, a metasurface can generate non-classical phase distributions for the transmitted and reflected electromagnetic waves at its interface. Thus, it offers more flexibility to control…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
Differentiable physics is a powerful approach to learning and control problems that involve physical objects and environments. While notable progress has been made, the capabilities of differentiable physics solvers remain limited. We…
An iterative scheme is presented to solve analytically the relativistic fluid dynamics equations. The scheme is applied to longitudinal expansion, transversal symmetric and transversal asymmetric (triaxial) expansion as well. Within this…
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram…
We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…
We investigate the approximate dynamics of several differential equations when the solutions are restricted to a sparse subset of a given basis. The restriction is enforced at every time step by simply applying soft thresholding to the…
Metasurfaces are ultra-thin optical elements composed of engineered sub-wavelength structures that enable precise control of light. Their inverse design - determining a geometry that yields a desired optical response - is challenging due to…