New Framework for Computing a General Local Self-Diffusion Coefficient Using Statistical Mechanics

Hunter, Michelle A.; Demir, Barış; Petersen, Charlotte F.; Bernhardt, Debra Joy

doi:10.1021/acs.jctc.2c00207

Cited by 8 publications

(12 citation statements)

References 32 publications

(54 reference statements)

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“…The MSD and self-diffusion coefficient (D i ) are considered to evaluate the molecule's mobility 52 , 53 , the definition of MSD can be found in our previous study 54 . The following equation is applied to appraise the MSD 55 , 56 : where r i (Δt) − r i (0) is defined as the distance traveled by COM of the particle i over some time interval of length.…”

Section: Methodsmentioning

confidence: 99%

Validation of an MD simulation approach for electrical field responsive micelles and their application in drug delivery

Razavi

Raissi

Farzad

2023

Sci Rep

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In the current work, a new type of micelle is designed that has active connectivity in respond to exterior stimulus and the desired water solubility. Two end-ornamented homopolymers, polystyrene-beta-cyclodextrin (PS-β-CD) and polyethylene oxide-ferrocene (PE-FE), can aggregate as a supramolecular micelle (PS-β-CD/PE-FE) by the guest–host interactions. Our results showed that the Lennard–Jones and hydrophobic interactions are the main powerful forces for the micelle formation process. It was found that the electrical field plays a role as a driving force in the reversible assembly-disassembly of the micellar system. Moreover, for the first time, we examined the PS-β-CD/PE-FE micelle interaction as a drug delivery system with anastrozole (ANS) and mitomycin C (MIC) anti-cancer drugs. The investigation of the total energy between PS-β-CD/PE-FE micelle and drugs predicts the drug adsorption process as favorable (Etotal = − 638.67 and − 259.80 kJ/mol for the Micelle@ANS and Micelle@MIC complexes, respectively). Our results offer a deep understanding of the micelle formation process, the electrical field-respond, and drug adsorption behaviors of the micelle. This simulation study has been accomplished by employing classical molecular dynamics calculation.

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Section: Methodsmentioning

confidence: 99%

Validation of an MD simulation approach for electrical field responsive micelles and their application in drug delivery

Razavi

Raissi

Farzad

2023

Sci Rep

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“…As will be discussed later, these approaches are still inherently ad hoc in the sense that observed mobility statistics are not guaranteed to conform to predictions based on the Smoluchowski equation 65 or the Kramers-Klein equation. 75 An an illustration, consider Hunter et al 87 who introduce a perturbation to the Hamiltonian given by…”

Section: 2mentioning

confidence: 99%

Estimating Position-Dependent and Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories: Existing Methods and Future Outlook

Domingues,

Coifman,

Haji-Akbari

2024

J. Chem. Theory Comput.

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Confinement can substantially alter the physicochemical properties of materials by breaking translational isotropy and rendering all physical properties positiondependent. Molecular dynamics (MD) simulations have proven instrumental in characterizing such spatial heterogeneities and probing the impact of confinement on materials' properties. For static properties, this is a straightforward task and can be achieved via simple spatial binning. Such an approach, however, cannot be readily applied to transport coefficients due to lack of natural extensions of autocorrelations used for their calculation in the bulk. The prime example of this challenge is diffusivity, which, in the bulk, can be readily estimated from the particles' mobility statistics, which satisfy the Fokker−Planck equation. Under confinement, however, such statistics will follow the Smoluchowski equation, which lacks a closed-form analytical solution. This brief review explores the rich history of estimating profiles of the diffusivity tensor from MD simulations and discusses various approximate methods and algorithms developed for this purpose. Besides discussing heuristic extensions of bulk methods, we overview more rigorous algorithms, including kernel-based methods, Bayesian approaches, and operator discretization techniques. Additionally, we outline methods based on applying biasing potentials or imposing constraints on tracer particles. Finally, we discuss approaches that estimate diffusivity from mean first passage time or committor probability profiles, a conceptual framework originally developed in the context of collective variable spaces describing rare events in computational chemistry and biology. In summary, this paper offers a concise survey of diverse approaches for estimating diffusivity from MD trajectories, highlighting challenges and opportunities in this area.

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“…Although the sum of the cross term ∑ i≠j c i c j 〈v i (t)v j (0)〉 becomes zero in the conventional CD-NEMD (c i = (-1) i ) 5,16 , calculations of ionic conductivities must include the cross term to be consistent with the Green-Kubo formulation (Eq. ( 1)).…”

Section: Ccd-nemd For Computing Conductivities With Ion-ion Correlationmentioning

confidence: 99%

“…We discuss the applicability of CCD-NEMD for interfacial conduction in grain-boundary systems and composite electrolytes. NEMD can be used to calculate interfacial conductivities by defining the local flux in a straightforward manner, as proposed in previous studies 11,16 . We constructed the energetically favorable Σ3(112) grain-boundary structure 32,33 .…”

Section: Ccd-nemd For Interfacial Conduction: Llzo Grain Boundarymentioning

confidence: 99%

Nonequilibrium molecular dynamics for accelerated computation of ion–ion correlated conductivity beyond Nernst–Einstein limitation

et al. 2023

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Condensed matters with high ionic conductivities are crucial in various solid devices such as solid-state batteries. The conduction is characterized by the cooperative ionic motion associated with the high carrier density. However, the high cost of computing correlated ionic conductivities has forced almost all ab initio molecular dynamics (MD) to rely on the Nernst–Einstein dilute-solution approximation, which ignores the cross-correlation effect. Here we develop a chemical color-diffusion nonequilibrium MD (CCD-NEMD) method, which enables to calculate the correlated conductivities with fewer sampling steps than the conventional MD. This CCD-NEMD is demonstrated to well evaluate the conductivities in the representative solid electrolyte bulk Li10GeP2S12 and Li7La3Zr2O12. We also applied CCD-NEMD to the grain boundary of Li7La3Zr2O12 and demonstrated its applicability for calculating interfacial local conductivities, which is essential for investigating grain boundaries and composite electrolytes. CCD-NEMD can provide further accurate understanding of ionics with ionic correlations and promote developing solid devices.

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New Framework for Computing a General Local Self-Diffusion Coefficient Using Statistical Mechanics

Cited by 8 publications

References 32 publications

Validation of an MD simulation approach for electrical field responsive micelles and their application in drug delivery

Validation of an MD simulation approach for electrical field responsive micelles and their application in drug delivery

Estimating Position-Dependent and Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories: Existing Methods and Future Outlook

Nonequilibrium molecular dynamics for accelerated computation of ion–ion correlated conductivity beyond Nernst–Einstein limitation

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