Related papers: A Conjecture about Molecular Dynamics
We survey an area of recent development, relating dynamics to theoretical computer science. We discuss the theoretical limits of simulation and computation of interesting quantities in dynamical systems. We will focus on central objects of…
The concept of random dynamical system is a comparatively recent development combining ideas and methods from the well developed areas of probability theory and dynamical systems. Due to our inaccurate knowledge of the particular physical…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Excellent computer simulations are done for a purpose. The most valid purposes are to explore uncharted territory, to resolve a well-posed scientific or technical question, or to make a design choice. Stand-alone modeling can serve the…
Molecular science is governed by the dynamics of electrons, atomic nuclei, and their interaction with electromagnetic fields. A reliable physicochemical understanding of these processes is crucial for the design and synthesis of chemicals…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Many real-world dynamic systems, both natural and artificial, are understood to be performing computations. For artificial dynamic systems, explicitly designed to perform computation - such as digital computers - by construction, we can…
The intuition that a long history is required for the emergence of complexity in natural systems is formalized using the notion of depth. The depth of a system is defined in terms of the number of parallel computational steps needed to…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
The claim that there is an inconsistency of quantum-classical dynamics [1] is investigated. We point out that a consistent formulation of quantum and classical dynamics which can be used to describe quantum measurement processes is already…
Atomistic simulations with methods such as molecular dynamics are extremely powerful tools to understand nanoscale dynamical behavior. The resulting trajectories, by the virtue of being embedded in a high-dimensional configuration space,…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Classical molecular dynamics (MD) simulations will be able to reach sampling in the second timescale within five years, producing petabytes of simulation data at current force field accuracy. Notwithstanding this, MD will still be in the…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
The beauty of physics is that there is usually a conserved quantity in an always-changing system, known as the constant of motion. Finding the constant of motion is important in understanding the dynamics of the system, but typically…
Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…