Related papers: Variationally Optimized Free Energy Flooding for R…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment is developed and applied to water. The idea for treating charges as variables is based on the concept of…
The incorporation of stochastic loads and generation into the operation of power grids gives rise to an exposure to stochastic risk. This risk has been addressed in prior work through a variety of mechanisms, such as scenario generation or…
A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, {\it rotors}, and…
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…
Transition path sampling is a method for estimating the rates of rare events in molecular systems based on the gradual transformation of a path distribution containing a small fraction of reactive trajectories into a biased distribution in…
In this paper, a statistical physical derivation of thermodynamically consistent fluid mechanical equations is presented for non-isothermal viscous molecular fluids. The coarse-graining process is based on (i) the adiabatic expansion of the…
We present numerical solutions to the extended Doering-Constantin variational principle for upper bounds on the energy dissipation rate in turbulent plane Couette flow. Using the compound matrix technique in order to reformulate this…
Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process…
This work investigates variational frameworks for modeling stochastic dynamics in incompressible fluids, focusing on large-scale fluid behavior alongside small-scale stochastic processes. The authors aim to develop a coupled system of…
We introduce a method for elucidating and modifying the functionality of systems dominated by rare events that relies on the automated tuning of their underlying free energy surface. The proposed approach seeks to construct collective…
Ordinary differential equations are widely-used in the field of systems biology and chemical engineering to model chemical reaction networks. Numerous techniques have been developed to estimate parameters like rate constants, initial…
A variety of enhanced sampling methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is…
Hybrid kinetic-MHD models describe the interaction of an MHD bulk fluid with an ensemble of hot particles, which is described by a kinetic equation. When the Vlasov description is adopted for the energetic particles, different Vlasov-MHD…
This dissertation is about the study of three important issues in the theory of relativistic fluid dynamics: the stability of dissipative fluid dynamics, the shear viscosity, and fluid dynamics with triangle anomaly.(1)The second order…
Flow maps enable high-quality image generation in a single forward pass. However, unlike iterative diffusion models, their lack of an explicit sampling trajectory impedes incorporating external constraints for conditional generation and…
We present molecular dynamics simulations of mono- or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met…
In this paper, we introduce a diffuse interface model for describing the dynamics of mixtures involving multiple (two or more) phases. The coupled hydrodynamical system is derived through an energetic variational approach. The total energy…
Variational quantum metrology represents a powerful tool for optimizing generic estimation strategies, combining the principles of variational optimization with the techniques of quantum metrology. Such optimization procedures result…
In this article, variational state estimation is examined from the dynamic programming perspective. This leads to two different value functional recursions depending on whether backward or forward dynamic programming is employed. The result…