scholarly journals Hybrid Coarse-Graining Approach for Lipid Bilayers at Large Length and Time Scales

2009 ◽  
Vol 113 (13) ◽  
pp. 4413-4424 ◽  
Author(s):  
Gary S. Ayton ◽  
Gregory A. Voth
Keyword(s):  
Lipid Bilayers ◽  
Time Scales ◽  
Coarse Graining ◽  
Large Length

SYMBOLIC DYNAMICS, COARSE GRAINING AND THE MONITORING OF COMPLEX SYSTEMS

2011 ◽  
Vol 21 (12) ◽  
pp. 3465-3475 ◽  
Author(s):  
VASILEIOS BASIOS ◽  
DÓNAL MAC KERNAN
Keyword(s):  
Dynamical Systems ◽  
Nonlinear Systems ◽  
Complex Systems ◽  
Error Estimates ◽  
Time Scales ◽  
Symbolic Dynamics ◽  
Prediction Error ◽  
Probabilistic Approach ◽  
Coarse Graining ◽  
Complex Nonlinear Systems

Coarse graining techniques and their associated symbolic dynamics are reviewed with a focus on probabilistic aspects of complex dynamical systems. The probabilistic approach initiated by Nicolis and coworkers has been elaborated. One of the major issues when dealing with the dynamics of complex nonlinear systems, the fact that the inherent time-scales of the unfolding phenomena are not well separated, is brought into focus. Recent results related to this interdependence, which is one of the most characteristic aspects of complexity and a major challenge in prediction, error estimates and monitoring of nonlinear complex systems, are discussed.

Systematic Coarse-graining and Multiscale Modeling of Soft Matter [PowerPoint Submission]

2006 ◽  
Vol 978 ◽  
Author(s):  
Gregory A. Voth
Keyword(s):  
Multiscale Modeling ◽  
Time Scales ◽  
Continuum Mechanics ◽  
Liquid State ◽  
Soft Matter ◽  
Coarse Graining ◽  
Mesoscale Dynamics ◽  
Computational Methodology ◽  
Primary Focus ◽  
Mesoscale Simulations

AbstractA multiscale theoretical and computational methodology will be presented for describing liquid state, biomolecular, and nanoparticle systems across multiple length- and time-scales. The approach provides an interface between atomistic molecular simulations, mesoscale dynamics, and continuum mechanics. The underlying methodology couples atomistic-level simulations with mesoscale simulations which, in turn, can be bridged to continuum-level modeling where necessary. A new and systematic multiscale coarse-graining strategy for linking the atomistic-scale interactions to the mesoscale will be the primary focus of the presentation. Applications of the overall methodology will be given.

RENORMALIZATION OF ATOMISTIC GROWTH MODELS

2008 ◽  
Vol 22 (22) ◽  
pp. 3721-3755 ◽  
Author(s):  
CHRISTOPH A. HASELWANDTER ◽  
DIMITRI D. VVEDENSKY
Keyword(s):  
Time Scales ◽  
Initial Conditions ◽  
Growth Models ◽  
Kinetic Monte Carlo ◽  
General Procedure ◽  
Lattice Models ◽  
Coarse Graining ◽  
General Terms ◽  
Kinetic Monte Carlo Simulations ◽  
Transition Rules

We review a general procedure for the multiscale analysis of atomistic lattice models of fluctuating interfaces driven by the deposition of new material. Beginning with a lattice Langevin formulation of site fluctuations, stochastic differential equations are derived by regularizing the lattice transition rules. Subsequent coarse graining is accomplished by applying the renormalization group, which yields trajectories from initial conditions determined by the regularized atomistic models. These trajectories correspond to hierarchies of continuum equations that describe the original lattice models over expanding length and time scales as the extent of coarse graining increases. This provides a systematic method for the derivation of continuum equations from the transition rules of lattice models appropriate for any length and time scales, and thereby establishes a quantitative link between atomistic transition rules and the collective behavior of the system. The results obtained with this method are confirmed by all available kinetic Monte Carlo simulations and, in some cases, have provided new interpretations of previous experimental observations. In this review, we first discuss the elements of our multiscale method in general terms, and then illustrate their implementation for specific growth models.

scholarly journals Time scales for dynamical relaxation to the Born rule

2011 ◽  
Vol 468 (2140) ◽  
pp. 990-1013 ◽  
Author(s):  
M. D. Towler ◽  
N. J. Russell ◽  
Antony Valentini
Keyword(s):  
Wave Function ◽  
Time Scales ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Relativistic Quantum Mechanics ◽  
Inflationary Cosmology ◽  
Electron Trajectory ◽  
Born Rule ◽  
Pilot Wave ◽  
De Broglie Bohm

We illustrate through explicit numerical calculations how the Born rule probability densities of non-relativistic quantum mechanics emerge naturally from the particle dynamics of de Broglie–Bohm pilot-wave theory. The time evolution of a particle distribution initially not equal to the absolute square of the wave function is calculated for a particle in a two-dimensional infinite potential square well. Under the de Broglie–Bohm ontology, the box contains an objectively existing ‘pilot wave’ which guides the electron trajectory, and this is represented mathematically by a Schrödinger wave function composed of a finite out-of-phase superposition of M energy eigenstates (with M ranging from 4 to 64). The electron density distributions are found to evolve naturally into the Born rule ones and stay there; in analogy with the classical case this represents a decay to ‘quantum equilibrium’. The proximity to equilibrium is characterized by the coarse-grained subquantum H -function which is found to decrease roughly exponentially towards zero over the course of time. The time scale τ for this relaxation is calculated for various values of M and the coarse-graining length ε . Its dependence on M is found to disagree with an earlier theoretical prediction. A power law, τ ∝ M −1 , is found to be fairly robust for all coarse-graining lengths and, although a weak dependence of τ on ε is observed, it does not appear to follow any straightforward scaling. A theoretical analysis is presented to explain these results. This improvement in our understanding of time scales for relaxation to quantum equilibrium is likely to be of use in the development of models of relaxation in the early Universe, with a view to constraining possible violations of the Born rule in inflationary cosmology.

scholarly journals HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multi-Scale Simulations of Soft Matter

2021 ◽  
Author(s):  
Morten Ledum ◽  
Samiran Sen ◽  
Xinmeng Li ◽  
Manuel Carrer ◽  
Yu Feng ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Self Assembly ◽  
Soft Matter ◽  
Time Integration ◽  
Hamiltonian Formulation ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Physical Force ◽  
Particle Field ◽  
Hybrid Particle

We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics (hPF). The methodology is based on tunable, grid-independent length-scale of coarse graining, obtained by filtering particle densities in reciprocal space. This enables systematic convergence of energies and forces by grid refinement, also eliminating non-physical force aliasing. Separating the time integration of fast modes associated with internal molecular motion, from slow modes associated with their density fields, we implement the first time-reversible hPF simulations. HyMD comprises the optional use of explicit electrostatics, which, in this formalism, corresponds to the long-range potential in Particle-Mesh Ewald. We demonstrate the ability of HhPF to perform simulations in the microcanonical and canonical ensembles with a series of test cases, comprising lipid bilayers and vesicles, surfactant micelles, and polypeptide chains, comparing our results to established literature. An on-the-fly increase of the characteristic coarse graining length significantly speeds up dynamics, accelerating self-diffusion and leading to expedited aggregation. Exploiting this acceleration, we find that the time scales involved in the self-assembly of polymeric structures can lie in the tens to hundreds of picoseconds instead of the multi microsecond regime observed with comparable coarse-grained models.

scholarly journals Label-free and charge-sensitive dynamic imaging of lipid membrane hydration on millisecond time scales

2018 ◽  
Vol 115 (16) ◽  
pp. 4081-4086 ◽  
Author(s):  
Orly B. Tarun ◽  
Christof Hannesschläger ◽  
Peter Pohl ◽  
Sylvie Roke
Keyword(s):  
Membrane Potential ◽  
Lipid Bilayers ◽  
Time Scales ◽  
Lipid Membrane ◽  
Mechanical Stability ◽  
Second Harmonic ◽  
Dynamic Imaging ◽  
Hydrophobic Core ◽  
Label Free ◽  
Membrane Function

Biological membranes are highly dynamic and complex lipid bilayers, responsible for the fate of living cells. To achieve this function, the hydrating environment is crucial. However, membrane imaging typically neglects water, focusing on the insertion of probes, resonant responses of lipids, or the hydrophobic core. Owing to a recent improvement of second-harmonic (SH) imaging throughput by three orders of magnitude, we show here that we can use SH microscopy to follow membrane hydration of freestanding lipid bilayers on millisecond time scales. Instead of using the UV/VIS resonant response of specific membrane-inserted fluorophores to record static SH images over time scales of >1,000 s, we SH imaged symmetric and asymmetric lipid membranes, while varying the ionic strength and pH of the adjacent solutions. We show that the nonresonant SH response of water molecules aligned by charge−dipole interactions with charged lipids can be used as a label-free probe of membrane structure and dynamics. Lipid domain diffusion is imaged label-free by means of the hydration of charged domains. The orientational ordering of water is used to construct electrostatic membrane potential maps. The average membrane potential depends quadratically on an applied external bias, which is modeled by nonlinear optical theory. Spatiotemporal fluctuations on the order of 100-mV changes in the membrane potential are seen. These changes imply that membranes are very dynamic, not only in their structure but also in their membrane potential landscape. This may have important consequences for membrane function, mechanical stability, and protein/pore distributions.

Observation of Concanavalin-A receptors on hydrated planar erythrocyte membrane film by in situ electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 608-609
Author(s):  
Neng-Bo He ◽  
S.W. Hui
Keyword(s):  
Lipid Bilayers ◽  
Erythrocyte Membrane ◽  
Lipid Membranes ◽  
Surface Film ◽  
Biological Membranes ◽  
Electron Microscopic Observation ◽  
Electron Microscopic ◽  
Black Lipid Membranes ◽  
Fine Mesh ◽  
Planar Films

Monolayers and planar "black" lipid membranes have been widely used as models for studying the structure and properties of biological membranes. Because of the lack of a suitable method to prepare these membranes for electron microscopic observation, their ultrastructure is so far not well understood. A method of forming molecular bilayers over the holes of fine mesh grids was developed by Hui et al. to study hydrated and unsupported lipid bilayers by electron diffraction, and to image phase separated domains by diffraction contrast. We now adapted the method of Pattus et al. of spreading biological membranes vesicles on the air-water interfaces to reconstitute biological membranes into unsupported planar films for electron microscopic study. hemoglobin-free human erythrocyte membrane stroma was prepared by hemolysis. The membranes were spreaded at 20°C on balanced salt solution in a Langmuir trough until a surface pressure of 20 dyne/cm was reached. The surface film was repeatedly washed by passing to adjacent troughs over shallow partitions (fig. 1).

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