The physics of open systems for the simulation of complex molecular environments in soft matter

Ciccotti, Giovanni; Site, Luigi Delle

doi:10.1039/c8sm02523a

Cited by 21 publications

(28 citation statements)

References 74 publications

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“…work, the capability of the method to deliver satisfactory results is a technical verification of its capacity for simulating large complex molecular environments [8]. Here, we will consider a DPPC bilayer whose full atomistic system of reference consists of 180 (90 per leaflet) DPPC molecules [see Figs.…”

Section: B Definition Of the Relevant Atomistic Degrees Of Freedom Vmentioning

confidence: 99%

“…We suggest the reader consult the cited references for the specific details. Originally, the TR region was composed of interacting coarse-grained molecules, and the coupling with the AT region was achieved through interpolation of atomistic and coarse-grained forces via a space-dependent smoothing function in (see, e.g., [8,10]). The region is defined by the cutoff of the atomistic potential.…”

Section: Basic Principles Of Adress and The Criteria For An Openmentioning

confidence: 99%

“…The extreme simplification of the computational setup became possible through the mapping of the algorithm onto a theoretical model of open system. Such a model fixes a series of conditions which are sufficient to assure that the physics of the AT region is correct and, in the limit of large TR and AT regions compared to , one has a grand-canonical-like ensemble for AT [8] (GC-AdResS). The application of the thermodynamic force in is one of such conditions.…”

Section: Basic Principles Of Adress and The Criteria For An Openmentioning

confidence: 99%

“…As discussed before, the three conditions that our adaptive setup needs to satisfy in order to define a proper open region for the AT portion of AdResS [8,10] concern (i) a basic structural property: the water density in the AT + region should be equal, within some numerical accuracy, to the fully atomistic reference value. This criterion assures that, by the action of the thermodynamic force in , one is at the same thermodynamic state point of the system of reference.…”

Section: A Verification Of Mandatory Conditions For a Physically Meamentioning

confidence: 99%

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Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation

Whittaker

Site

2019

Phys. Rev. Research

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We analyze structural properties of hydration for a biological membrane with the open boundary adaptive resolution molecular dynamics approach in its latest version. A large region of noninteracting pointlike particles (tracers) acts as a reservoir of molecules and energy for the atomistically resolved membrane-water interface. The drastic simplification of the environment and its simple coupling to the high-resolution region has been successfully tested in a previous work on pure liquid water, and this work represents the method's first application to a system with high structural complexity. The successful results and novel methodology allow us to suggest a complementary view to the controversial question of the definition of the hydration shell for a membrane. The adaptive resolution technique allows for a physically well-founded statistical mechanics definition of the hydration shell by quantifying the minimal size of the region where the atomistic resolution of the molecules is strictly required while the rest of the system plays the role of a generic, structureless thermodynamic reservoir.

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Section: B Definition Of the Relevant Atomistic Degrees Of Freedom Vmentioning

confidence: 99%

Section: Basic Principles Of Adress and The Criteria For An Openmentioning

confidence: 99%

Section: Basic Principles Of Adress and The Criteria For An Openmentioning

confidence: 99%

Section: A Verification Of Mandatory Conditions For a Physically Meamentioning

confidence: 99%

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Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation

Whittaker

Site

2019

Phys. Rev. Research

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“…5,6 The study of the mechanism of the folding and unfolding of the protein structure is benecial for new research and innovation in the eld of biochemistry. 7 Generally, the protein gets denatured at highly acidic or low pH, resulting in pH-dependent, protein misfolding associated biological imbalances such as the formation of amyloid brils in the case of Alzheimer's disease and type-2 diabetes. 4,[8][9][10] The conformational changes in the protein structure causes subtle changes in its potential energy, which is reected by the unfolding or folding of the protein.…”

Section: Introductionmentioning

confidence: 99%

A molecular simulation approach towards the development of universal nanocarriers by studying the pH- and electrostatic-driven changes in the dynamic structure of albumin

2020

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Molecular Dynamics

Wieczorek¹,

Niedziałek²

2020

Encyclopedia of Life Sciences

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Molecular dynamics (MD) is a handy computer simulation method which unveils principles of a large variety of fundamental processes by mimicking the real life perpetual motion of atoms triggered by interatomic forces. In MD, these forces are expressed through analytical functions and associated parameters, which are commonly referred to as the force field. The forces' effect on the movement of atoms is determined by Newton's second law. Most importantly, MD simulations are able to retrace the exact trajectories of interacting atoms by following their spatial evolution in time from a defined initial configuration. The resulting integrated trajectory of the system can be visualised and analysed with rigorous mathematical expressions of statistical mechanics, which relate averaged microscopic states to macroscopic properties relevant to the problem at hand. Key Concepts Molecular dynamics is a computation tool successfully used to unveil principles of a large variety of fundamental processes down to the atomic resolution. Thanks to recent advances in computer simulations, atomistic MD can reach millisecond timescales, thus emerging as a powerful alternative method that successfully complements experimental measurements in biology. Computational efficiency of molecular dynamics algorithms continues to pose challenges. The collective efforts of many groups of researchers have enabled a great deal of force fields applied to many problems in biology. Biomolecular simulations require the presence of solvent; hence, a reliable representation of water is crucial for achieving realistic results. Several specialised methods stemming from MD allow to investigate various processes of biomolecules: REMD, SMD and TMD.

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The physics of open systems for the simulation of complex molecular environments in soft matter

Abstract: Multiscale molecular dynamics of open systems represents a powerful tool of investigation in soft matter.

Cited by 21 publications

References 74 publications

Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation

Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation

A molecular simulation approach towards the development of universal nanocarriers by studying the pH- and electrostatic-driven changes in the dynamic structure of albumin

Molecular Dynamics

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