Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory

Qi, Shuanhu; Schmid, Friederike

doi:10.1039/c7sm01749a

Cited by 12 publications

(12 citation statements)

References 71 publications

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“…We focused here on the equilibrium simulations, but arbitrary external boundary conditions could be imposed that would just as well permit the simulation of nonequilibrium dynamics (59). The framework presented could be used furthermore as an interface to connect MD with continuum hydrodynamics (85)(86)(87)(88)(89)(90)(91)(92)(93)(94).…”

Section: Discussionmentioning

confidence: 99%

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

Zavadlav

Sablić

Podgornik

et al. 2018

Biophysical Journal

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The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system's electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.

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Section: Discussionmentioning

confidence: 99%

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

Zavadlav

Sablić

Podgornik

et al. 2018

Biophysical Journal

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“…To avoid the intervals determined by altered cluster material this hybrid method is used. This is helpful in improving the clustering performance [33]. This algorithm uses the global optimization.…”

Section: Local Approachmentioning

confidence: 99%

An Examination of Machine Learning Algorithms for Missing Values Imputation

2019

IJITEE

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In gene expression studies missing values have been a common problem. It has an important consequence on the explanation of the final data. Numerous Bioinformatics examination tools that are used for cancer prediction includes the dataset matrix. Hence, it is necessary to resolve this problem of missing values imputation. Our research paper presents a review of missing values imputation approaches. It represents the research and imputation of missing values in gene expression data. By using the local or global correlation of the data we focus mostly on the contrast of the algorithms. We considered the algorithms in a global, hybrid, local, and knowledge-based technique. Additionally, we presented the different approaches with a suitable assessment. The purpose of our review article is to focus on the developments of current techniques. For scientists rather applying different or newly develop algorithms with the identical functional goal. We want an adaptation of algorithms to the characteristics of the data".

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“…Anero et al (2013) have constructud an approach that they call functional thermodynamics, which represents a generalization of dynamic density functional theory to non-isothermal situations. DDFT has also been used to describe polymeric systems (Qi and Schmid, 2017). Archer and Rauscher (2004b) have aimed to clarify confusions in the literature as to whether or not dynamical density functional theories for the one-body density of a classical Brownian fluid should contain a stochastic noise term.…”

Section: H Approximate Free Energy Functionalsmentioning

confidence: 99%

Power functional theory for Newtonian many-body dynamics

Schmidt

2018

The Journal of Chemical Physics

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We construct a variational theory for the inertial dynamics of classical many-body systems out of equilibrium. The governing (power rate) functional depends on three time- and space-dependent one-body distributions, namely, the density, the particle current, and the time derivative of the particle current. The functional is minimized by the true time derivative of the current. Together with the continuity equation, the corresponding Euler-Lagrange equation uniquely determines the time evolution of the system. An adiabatic approximation introduces both the free energy functional and the Brownian free power functional, as is relevant for liquids governed by molecular dynamics at constant temperature. The forces beyond the Brownian power functional are generated from a superpower (above the overdamped Brownian) functional.

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Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory

Cited by 12 publications

References 71 publications

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

An Examination of Machine Learning Algorithms for Missing Values Imputation

Power functional theory for Newtonian many-body dynamics

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