Fluctuating hydrodynamics for multiscale simulation of inhomogeneous fluids: Mapping all-atom molecular dynamics to capillary waves

2011 ◽  
Vol 135 (4) ◽  
pp. 044111 ◽  
Author(s):  
Barry Z. Shang ◽  
Nikolaos K. Voulgarakis ◽  
Jhih-Wei Chu
Keyword(s):  
Molecular Dynamics ◽  
Multiscale Simulation ◽  
Capillary Waves ◽  
Fluctuating Hydrodynamics ◽  
Inhomogeneous Fluids

Multiscale Simulations of Thermoelectric Properties of PBTE

2008 ◽  
Author(s):  
Bo Qiu ◽  
Hua Bao ◽  
Xiulin Ruan
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermoelectric Properties ◽  
Transport Coefficients ◽  
Multiscale Simulation ◽  
Full Potential ◽  
Boltzmann Transport ◽  
Pair Potentials ◽  
Dynamics Simulations

In this paper, thermoelectric properties of bulk PbTe are calculated using first principles calculations and molecular dynamics simulations. The Full Potential Linearized Augmented Plane Wave (FP-LAPW) method is first employed to calculate the PbTe band structure. The transport coefficients (Seebeck coefficient, electrical conductivity, and electron thermal conductivity) are then computed using Boltzmann transport equation (BTE) under the constant relaxation time approximation. Interatomic pair potentials in the Buckingham form are also derived using ab initio effective charges and total energy data. The effective interatomic pair potentials give excellent results on equilibrium lattice parameters and elastic constants for PbTe. The lattice thermal conductivity of PbTe is then calculated using molecular dynamics simulations with the Green-Kubo method. In the end, the figure of merit of PbTe is computed revealing the thermoelectric capability of this material, and the multiscale simulation approach is shown to have the potential to identify novel thermoelectric materials.

scholarly journals Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale

2020 ◽  
Author(s):  
Chenghan Li ◽  
Zhi Yue ◽  
L. Michel Espinoza-Fonseca ◽  
Gregory A. Voth
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Sarcoplasmic Reticulum ◽  
Binding Site ◽  
Proton Transport ◽  
Computational Study ◽  
Multiscale Simulation ◽  
Proton Pumping ◽  
Reactive Molecular Dynamics ◽  
Free Energy Sampling

ABSTRACTThe sarcoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions from the cytoplasm to the reticulum lumen at the expense of ATP hydrolysis. In addition to transporting Ca2+, SERCA facilitates bidirectional proton transport across the sarcoplasmic reticulum to maintain the charge balance of the transport sites and to balance the charge deficit generated by the exchange of Ca2+. Previous studies have shown the existence of a transient water-filled pore in SERCA that connects the Ca2+-binding sites with the lumen, but the capacity of this pathway to sustain passive proton transport has remained unknown. In this study, we used the multiscale reactive molecular dynamics (MS-RMD) method and free energy sampling to quantify the free energy profile and timescale of the proton transport across this pathway while also explicitly accounting for the dynamically coupled hydration changes of the pore. We find that proton transport from the central binding site to the lumen has a microsecond timescale, revealing a novel passive cytoplasm-to-lumen proton flow beside the well-known inverse proton countertransport occurring in active Ca2+ transport. We propose that this proton transport mechanism is operational and serves as a functional conduit for passive proton transport across the sarcoplasmic reticulum.SIGNIFICANCEMultiscale reactive molecular dynamics combined with free energy sampling was applied to study proton transport through a transient water pore connecting the Ca2+-binding site to the lumen in SERCA. This is the first computational study of this large biomolecular system that treats the hydrated excess proton and its transport through water structures and amino acids explicitly. When also correctly accounting for the hydration fluctuations of the pore, it is found that a transiently hydrated channel can transport protons on a microsecond timescale. These results quantitatively support the hypothesis of the proton intake into the sarcoplasm via SERCA, in addition to the well-known proton pumping by SERCA to the cytoplasm along with Ca2+ transport.

Multiscale Investigation of Thickness Dependent Melting Thresholds of Nickel Film Under Femtosecond Laser Heating

2018 ◽  
Author(s):  
Pengfei Ji ◽  
Mengzhe He ◽  
Yiming Rong ◽  
Yuwen Zhang ◽  
Yong Tang
Keyword(s):  
Molecular Dynamics ◽  
Femtosecond Laser ◽  
Multiscale Simulation ◽  
Nickel Film ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Model Description ◽  
Temperature Model ◽  
Laser Material Processing ◽  
Two Temperature

A multiscale modeling that integrates electronic scale ab initio quantum mechanical calculation, atomic scale molecular dynamics simulation, and continuum scale two-temperature model description of the femtosecond laser processing of nickel film at different thicknesses is carried out in this paper. The electron thermophysical parameters (heat capacity, thermal conductivity, and electron-phonon coupling factor) are calculated from first principles modeling, which are further substituted into molecular dynamics and two-temperature model coupled energy equations of electrons and phonons. The melting thresholds for nickel films of different thicknesses are determined from multiscale simulation. Excellent agreement between results from simulation and experiment is achieved, which demonstrates the validity of modeled multiscale framework and its promising potential to predict more complicate cases of femtosecond laser material processing. When it comes to process nickel film via femtosecond laser, the quantitatively calculated maximum thermal diffusion length provides helpful information on choosing the film thickness.

Fluctuating hydrodynamics and capillary waves

1983 ◽  
Vol 27 (5) ◽  
pp. 2577-2584 ◽  
Author(s):  
Martin Grant ◽  
Rashmi C. Desai
Keyword(s):  
Capillary Waves ◽  
Fluctuating Hydrodynamics

scholarly journals Binding of Ca2+-Independent C2 Domains to Lipid Membranes: a Multi-Scale Molecular Dynamics Study

2020 ◽  
Author(s):  
Andreas Haahr Larsen ◽  
Mark S.P. Sansom
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Md Simulations ◽  
Multiscale Simulation ◽  
Coarse Grained ◽  
Type I ◽  
Type Ii ◽  
Binding Modes ◽  
C2 Domains ◽  
Anionic Lipids

AbstractC2 domains facilitate protein-lipid interaction in cellular recognition and signalling processes. They possess a β-sandwich structure, with either type I or type II topology. C2 domains can interact with anionic lipid bilayers in either a Ca2+-dependent or a Ca2+-independent manner. The mechanism of recognition of anionic lipids by Ca2+-independent C2 domains is incompletely understood. We have used molecular dynamics (MD) simulations to explore the membrane interactions of six Ca2+– independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse grained MD simulations these C2 domains bound to lipid bilayers, forming transient interactions with zwitterionic (phosphatidylcholine, PC) bilayers compared to long lived interactions with anionic bilayers also containing either phosphatidylserine (PS) or PS and phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops (as is typically the case for Ca2+-dependent C2 domains). C2 domains interacted strongly (up to 120 kJ/mol) with membranes containing PIP2 causing the bound anionic lipids to clustered around the protein. The C2 domains bound less strongly to anionic membranes without PIP2 (<50 kJ/mol), and most weakly to neutral membranes (<33 kJ/mol). Productive binding modes were identified and further analysed in atomistic simulations. For PTEN and SHIP2, CG simulations were also performed of the intact enzymes (i.e. phosphatase domain plus C2 domain) with PIP2-contating bilayers and the roles of the two domains in membrane localization were compared. From a methodological perspective, these studies establish a multiscale simulation protocol for studying membrane binding/recognition proteins, capable of revealing binding modes alongside details of lipid binding affinity and specificity.

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