scholarly journals Wetting and cavitation pathways on nanodecorated surfaces

Soft Matter ◽  
2016 ◽  
Vol 12 (12) ◽  
pp. 3046-3055 ◽  
Author(s):  
Matteo Amabili ◽  
Emanuele Lisi ◽  
Alberto Giacomello ◽  
Carlo Massimo Casciola
Keyword(s):  
Molecular Dynamics ◽  
Rare Event ◽  
Cassie State

Rare event methods combined with molecular dynamics and macroscopic calculations reveal multiple pathways for the breakdown of the superhydrophobic Cassie state through wetting or cavitation.

scholarly journals Combining stochastic and deterministic approaches within high efficiency molecular simulations

2013 ◽  
Vol 11 (4) ◽  
Author(s):  
Bruno Escribano ◽  
Elena Akhmatskaya ◽  
Jon Mujika
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
High Efficiency ◽  
Rare Event ◽  
Molecular Simulations ◽  
Monte Carlo Sampling ◽  
Symplectic Integrators ◽  
Computational Time ◽  
Hybrid Monte Carlo ◽  
Event Dynamics

AbstractGeneralized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). While conventional hybrid Monte Carlo methods completely re-sample particle’s velocities between MD trajectories, our method suggests a partial velocity update procedure which keeps a part of the dynamic information throughout the simulation. We use shadow (modified) Hamiltonians, the asymptotic expansions in powers of the discretization parameter corresponding to timestep, which are conserved by symplectic integrators to higher accuracy than true Hamiltonians. We present the implementation of this method into the highly efficient MD code GROMACS and demonstrate its performance and accuracy on computationally expensive systems like proteins in comparison with the molecular dynamics techniques already available in GROMACS. We take advantage of the state-of-the-art algorithms adopted in the code, leading to an optimal implementation of the method. Our implementation introduces virtually no overhead and can accurately recreate complex biological processes, including rare event dynamics, saving much computational time compared with the conventional simulation methods.

scholarly journals Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics

2016 ◽  
Vol 195 ◽  
pp. 395-419 ◽  
Author(s):  
Mike O'Connor ◽  
Emanuele Paci ◽  
Simon McIntosh-Smith ◽  
David R. Glowacki
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Rare Event ◽  
Potential Of Mean Force ◽  
Good Evidence ◽  
Collective Variable ◽  
Rigid Body Dynamics ◽  
Free Energy Surface ◽  
Molecular Configuration ◽  
Free Energy Sampling

The past decade has seen the development of a new class of rare event methods in which molecular configuration space is divided into a set of boundaries/interfaces, and then short trajectories are run between boundaries. For all these methods, an important concern is how to generate boundaries. In this paper, we outline an algorithm for adaptively generating boundaries along a free energy surface in multi-dimensional collective variable (CV) space, building on the boxed molecular dynamics (BXD) rare event algorithm. BXD is a simple technique for accelerating the simulation of rare events and free energy sampling which has proven useful for calculating kinetics and free energy profiles in reactive and non-reactive molecular dynamics (MD) simulations across a range of systems, in both NVT and NVE ensembles. Two key developments outlined in this paper make it possible to automate BXD, and to adaptively map free energy and kinetics in complex systems. First, we have generalized BXD to multidimensional CV space. Using strategies from rigid-body dynamics, we have derived a simple and general velocity-reflection procedure that conserves energy for arbitrary collective variable definitions in multiple dimensions, and show that it is straightforward to apply BXD to sampling in multidimensional CV space so long as the Cartesian gradients ∇CV are available. Second, we have modified BXD to undertake on-the-fly statistical analysis during a trajectory, harnessing the information content latent in the dynamics to automatically determine boundary locations. Such automation not only makes BXD considerably easier to use; it also guarantees optimal boundaries, speeding up convergence. We have tested the multidimensional adaptive BXD procedure by calculating the potential of mean force for a chemical reaction recently investigated using both experimental and computational approaches – i.e., F + CD3CN → DF + D2CN in both the gas phase and a strongly coupled explicit CD3CN solvent. The results obtained using multidimensional adaptive BXD agree well with previously published experimental and computational results, providing good evidence for its reliability.

Molecular Dynamics of Rare-Event Electrostatic Channeling

2021 ◽  
Vol MA2021-01 (28) ◽  
pp. 976-976
Author(s):  
Yan Xie ◽  
Scott Calabrese Barton
Keyword(s):  
Molecular Dynamics ◽  
Rare Event

scholarly journals A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

2014 ◽  
Vol 169 ◽  
pp. 63-87 ◽  
Author(s):  
David R. Glowacki ◽  
Michael O'Connor ◽  
Gaetano Calabró ◽  
James Price ◽  
Philip Tew ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Physics Education ◽  
Computational Simulation ◽  
Rare Event ◽  
Dynamics Simulation ◽  
Gpu Acceleration ◽  
Human Form ◽  
Depth Sensors ◽  
Water Solvent

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human–computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3–4 orders of magnitude.

Rare event molecular dynamics simulations of plasma induced surface ablation

2014 ◽  
Vol 141 (7) ◽  
pp. 074706
Author(s):  
Onise Sharia ◽  
Jeffrey Holzgrafe ◽  
Nayoung Park ◽  
Graeme Henkelman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Rare Event ◽  
Surface Ablation ◽  
Dynamics Simulations

Spontaneous transition of a water droplet from the Wenzel state to the Cassie state: a molecular dynamics simulation study

2015 ◽  
Vol 17 (45) ◽  
pp. 30533-30539 ◽  
Author(s):  
Jiadao Wang ◽  
Shuai Chen ◽  
Darong Chen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Water Droplet ◽  
Dynamics Simulation ◽  
Spontaneous Transition ◽  
Transition Mechanism ◽  
Cassie State ◽  
Wenzel State ◽  
Influencing Parameters

Spontaneous transition from the Wenzel to Cassie state is achieved, and the transition mechanism and influencing parameters are analyzed.

Multiscale Molecular Dynamics Simulations of Nanostructured Materials

2007 ◽  
Vol 539-543 ◽  
pp. 2804-2809 ◽  
Author(s):  
Kenij Tsuruta ◽  
Atsushi Uchida ◽  
Chieko Totsuji ◽  
Hiroo Totsuji
Keyword(s):  
Molecular Dynamics ◽  
Grain Boundary ◽  
Hydrogen Diffusion ◽  
Reaction Pathway ◽  
Film Formation ◽  
Rare Event ◽  
High Energy ◽  
Long Time ◽  
Cu Thin Film ◽  
Dynamics Simulations

We present some attempts to simulate nanoscale phenomena, which involve different length-scales and time-scales, using multiscale molecular-dynamics approaches. To simulate realistically an impurity-segregated nanostructure, we have developed the hybrid quantum/classical approach. The method can describe seamlessly both dynamical changes of local chemical bonding and nanoscale atomic relaxations. We apply the method to hydrogen diffusion in Si grain boundary. We find that the hydrogen is strongly trapped in (001)Σ5 twist boundary below 1000K, whereas it starts diffusing along the grain boundary above 1000K. For long-time processes in nanostructure formation, we apply the stochastic-difference-equation method to accelerate the simulations for microstructure evolution. The method bridges the states separated by high-energy barriers in a configuration space by optimizing an action, defined as an error accumulation along a reaction pathway. As an example, a SDE simulation is performed for Cu thin-film formation via nanocluster deposition. We show that the method can be applied effectively to search for the long-time process which involves a rare event due to a large potential barrier between two atomic configurations.

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