Related papers: A Bell-Evans-Polanyi principle for molecular dynam…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
General parameters are highly desirable in the natural sciences - e.g., chemical reaction conditions that enable high yields across a range of related transformations. This has a significant practical impact since those general parameters…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
Bounce-averaged theories provide a framework for simulating relatively slow processes, such as collisional transport and quasilinear diffusion, by averaging these processes over the fast periodic motions of a particle on a closed orbit.…
We study equations for the mechanical movement of chains of identical particles in the plane interacting with their nearest-neighbors by bond stretching and by van der Waals and Coulomb forces. We find collinear and circular equilibria as…
Local optimization presents a promising approach to expensive, high-dimensional black-box optimization by sidestepping the need to globally explore the search space. For objective functions whose gradient cannot be evaluated directly,…
We study the law of the minimum of a Brownian bridge, conditioned to take specific values at specific points, and the law of the location of the minimum. They are used to compare some non-adaptive optimisation algorithms for black-box…
We discuss the structure of the equation of motion that governs nucleation processes at first order phase transitions. From the underlying microscopic dynamics of a nucleating system, we derive by means of a non-equilibrium projection…
The first goal of Vibration-Transit (V-T) theory was to construct a tractable approximate Hamiltonian from which the equilibrium thermodynamic properties of monatomic liquids can be calculated. The Hamiltonian for vibrations in an…
To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves…
We study a system of reflected Brownian motions on the positive half-line in which each particle has a drift toward the origin determined by the local times at the origin of all the particles. If this local time drift is too strong, such…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
In this short note we sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations…
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…
The rotating-wave approximation to light-matter interactions is widely used in the quantum electrodynamics Hamiltonian; however, its validity has long been a matter of debate. In this article, we explore the impact of the rotating-wave…
The accurate determination of the lowest electron attachment ($EA$) and ionization ($IP$) energies for molecules embedded in molecular junctions is important for correctly estimating, \emph{e.g.}, the magnitude of the currents ($I$) or the…
We investigate the possibility of stochastic acceleration of background low-energy electrons by turbulent plasma waves. We consider the resonant interaction of the charged particles with all branches of the transverse plasma waves…