Related papers: Custom Flow in Molecular Dynamics
Turbulent fluid flows exhibit a complex small-scale structure with frequently occurring extreme velocity gradients. Particles probing such swirling and straining regions respond with an intricate shape-dependent orientational dynamics,…
Quantifying energy flows at nanometer scales promises to guide future research in a variety of disciplines, from microscopic control and manipulation, to autonomously operating molecular machines. A general understanding of the…
We present the stochastic thermodynamics analysis of an open quantum system weakly coupled to multiple reservoirs and driven by a rapidly oscillating external field. The analysis is built on a modified stochastic master equation in the…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
Fluid dynamics in intrinsically curved geometries is encountered in many physical systems in nature, ranging from microscopic bio-membranes all the way up to general relativity at cosmological scales. Despite the diversity of applications,…
An accurate prediction of the translational and rotational motion of particles suspended in a fluid is only possible if a complete set of correlations for the force coefficients of fluid-particle interaction is known. The present study is…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
The rich and diverse dynamics of particle-based systems ultimately originates from the coupling of their degrees of freedom via internal interactions. To arrive at a tractable approximation of such many-body problems, coarse-graining is…
We consider a system of nonlinear partial differential equations describing the motion of an incompressible chemically reacting generalized Newtonian fluid in three space dimensions. The governing system consists of a steady…
We formulate a data-driven, physics-constrained closure method for coarse-scale numerical simulations of turbulent fluid flows. Our approach involves a closure scheme that is non-local both in space and time, i.e. the closure terms are…
Examples of self propulsion in strongly fluctuating environment is abound in nature, e.g., molecular motors and pumps operating in living cells. Starting from Langevin equation of motion, we develop a fluctuating thermodynamic description…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
In this work the issue of whether key energetic properties (nonlinear, exponential-type dissipation in the abscence of forcing and long-term stability under conditions of time dependent loading) are automatically inherited by deforming…
We present an energy-stable scheme for numerically approximating the governing equations for incompressible two-phase flows with different densities and dynamic viscosities for the two fluids. The proposed scheme employs a scalar-valued…
Forecasting conditional stochastic nonlinear dynamical systems is a fundamental challenge repeatedly encountered across the biological and physical sciences. While flow-based models can impressively predict the temporal evolution of…
Recent developments in surgical robotics have led to new advancements in the automation of surgical sub-tasks such as suturing, soft tissue manipulation, tissue tensioning and cutting. However, integration of dynamics to optimize these…
Accurate and efficient fluid flow models are essential for applications relating to many physical phenomena including geophysical, aerodynamic, and biological systems. While these flows may exhibit rich and multiscale dynamics, in many…
In the present paper a simple dynamical model for computing the osmotically driven fluid flow in a variety of complex, non equilibrium situations is derived from first principles. Using the Oberbeck-Boussinesq approximation, the basic…
A new and very general technique for simulating solid-fluid suspensions is described; its most important feature is that the computational cost scales linearly with the number of particles. The method combines Newtonian dynamics of the…
In this paper, we focus on investigating the influence on hydrodynamic factors of different coupled computational models describing the interaction between an incompressible fluid and two symmetric elastic or poroelastic structures. The…