Related papers: Simulational nanoengineering: Molecular dynamics i…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…
A thermostat of the Nose-Hoover type, based on relative velocities and a local definition of the temperature, is presented. The thermostat is momentum-conserving and Galilean-invariant, which should make it suitable for use in Dissipative…
In this research, atomistic molecular dynamics simulations are combined with mesoscopic phase-field computational methods in order to investigate phase-transformation in polycrystalline Aluminum microstructure. In fact, microstructural…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
Endoreversible engine cycles are a cornerstone of finite-time thermodynamics. We show that endoreversible Stirling engines operating with a one-component plasma as working medium run at maximal power output with the Curzon-Ahlborn…
A recently developed method of nanoclusters growth in a pulsed plasma is studied by means of molecular dynamics. A model that allows one to consider high-energy charged particles in classical molecular dynamics is suggested, and applied for…
To investigate the impact of fractional parameter on the thermodynamic behaviors of quantum systems, we incorporate fractional quantum mechanics into the cycle of a quantum Stirling heat engine and examine the influence of fractional…
The stability of a single-walled carbon nanotube placed on top of a catalytic nickel nanoparticle is investigated by means of molecular dynamics simulations. As a case study, we consider the $(12,0)$ nanotube consisting of 720 carbon atoms…
This paper introduces a smart model for intelligent energy management of steam generators which are utilized for steam generator and controlling the air to fuel ratio for steam generator all over the firing curve and transient mode…
A simple model for the reaction-driven propulsion of a small device is proposed as a model for (part of) a molecular machine in aqueous media. Motion of the device is driven by an asymmetric distribution of reaction products. The propulsive…
By converting energy into mechanical work, engines play a central role in most biological and technological processes. In particular, within the current trend towards the development of nanoscience and nanotechnology, microscopic engines…
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…
There are many exotic thermodynamic processes that are hard to study in nature. Here, we synthesize a structured environment to explore the extremes of thermodynamics. We present an engine running at extreme temperatures of above ten…
We describe the thermodynamic state of a highly confined single-phase and single-component fluid in a slit pore using Hill's thermodynamics of small systems. This theory was more recently named nanothermodynamics. We start by constructing…
The change in materials properties subjected to irradiation by highly energetic particles strongly depends on the irradiation dose rate. Atomistic simulations can in principle be used to predict microstructural evolution where experimental…
We investigate the dynamics of an active gel of bundled microtubules that is driven by clusters of kinesin molecular motors. Upon the addition of ATP, the coordinated action of thousands of molecular motors drives the gel to a highly…
Externally controlled motion of micro and nanomotors in a fluid environment constitutes a promising tool in biosensing, targeted delivery and environmental remediation. In particular, recent experiments have demonstrated that fuel-free…
Molecular machines consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an engine that "transduces" input energy into…
We investigate the structural and dynamical properties of binary aluminum-titanium liquid metallic alloys, as a function of temperature and composition. We make use of MD-simulations, using a transferable machine-learning potential…