Related papers: Exploring the Potential of Parallel Biasing in Fla…
Bayesian deep learning counts on the quality of posterior distribution estimation. However, the posterior of deep neural networks is highly multi-modal in nature, with local modes exhibiting varying generalization performance. Given a…
A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
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…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
We describe and implement iMapD, a computer-assisted approach for accelerating the exploration of uncharted effective Free Energy Surfaces (FES), and more generally for the extraction of coarse-grained, macroscopic information from…
Sampling the phase space of molecular systems -- and, more generally, of complex systems effectively modeled by stochastic differential equations -- is a crucial modeling step in many fields, from protein folding to materials discovery.…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
Distributed Lag Models (DLMs) and similar regression approaches such as MIDAS have been used for many decades in econometrics and more recently to investigate how poor air quality adversely affects human health. In this paper we describe…
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
We propose Parallelised Diffeomorphic Sampling-based Motion Planning (PDMP). PDMP is a novel parallelised framework that uses bijective and differentiable mappings, or diffeomorphisms, to transform sampling distributions of sampling-based…
Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…
We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as…
With the help of metadynamics it is possible to calculate efficiently the free energy of systems displaying high energy barriers as a function of few selected "collective variables". In doing this, the contribution of all the other degrees…
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
We present a simple model system with four hard disks moving in a circular region for which free energy landscapes can be directly calculated and visualized in two and three dimensions. We construct several energy landscapes for our system…
Computer simulations of a model glass-forming system are presented, which are particularly sensitive to the correlation between the dynamics and the topography of the potential energy landscape. This analysis clearly reveals that in the…