Journal ArticleDOI
Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations
TLDR
In this paper, the authors investigated the dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer using an all atom molecular dynamics simulation.Abstract:
Dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer are investigated using an all atom molecular dynamics simulation. Based upon the geometric criteria, continuously residing interface water molecules which form hydrogen bonds solely among themselves and then concertedly hydrogen bonded to carbonyl, phosphate, and glycerol head groups of DMPC are identified. The interface water hydrogen bonded to lipids shows slower relaxation rates for translational and rotational dynamics compared to that of the bulk water and is found to follow sub-diffusive and non-diffusive behaviors, respectively. The mean square displacements and the reorientational auto-correlation functions are slowest for the interfacial waters hydrogen bonded to the carbonyl oxygen since these are buried deep in the hydrophobic core among all interfacial water studied. The intermittent hydrogen bond auto-correlation functions are calculated, which allows breaking and reformations of the hydrogen bonds. The auto-correlation functions for interfacial hydrogen bonded networks develop humps during a transition from cage-like motion to eventual power law behavior of t−3/2. The asymptotic t−3/2 behavior indicates translational diffusion dictated dynamics during hydrogen bond breaking and formation irrespective of the nature of the chemical confinement. Employing reactive flux correlation analysis, the forward rate constant of hydrogen bond breaking and formation is calculated which is used to obtain Gibbs energy of activation of the hydrogen bond breaking. The relaxation rates of the networks buried in the hydrophobic core are slower than the networks near the lipid-water interface which is again slower than bulk due to the higher Gibbs energy of activation. Since hydrogen bond breakage follows a translational diffusion dictated mechanism, chemically confined hydrogen bond networks need an activation energy to diffuse through water depleted hydrophobic environments. Our calculations reveal that the slow relaxation rates of interfacial waters in the vicinity of lipids are originated from the chemical confinement of concerted hydrogen bond networks. The analysis suggests that the networks in the hydration layer of membranes dynamically facilitate the water mediated lipid-lipid associations which can provide insights on the thermodynamic stability of soft interfaces relevant to biological systems in the future.read more
Citations
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Journal ArticleDOI
Unusual confinement properties of a water insoluble small peptide hydrogel
Nilotpal Singha,Arpita Srivastava,Bapan Pramanik,Sahnawaz Ahmed,Payel Dowari,Sumit Chowdhuri,Basab Kanti Das,Ananya Debnath,Debapratim Das +8 more
TL;DR: A water insoluble peptide-hydrogel that shows unique compartmentalization by not allowing any exchange to and from the hydrogel and can protect enzymes from denaturation.
Book ChapterDOI
Overhauser Dynamic Nuclear Polarization for the Study of Hydration Dynamics, Explained.
John M. Franck,Songi Han +1 more
TL;DR: This chapter clarifies how the electron-nuclear dipolar coupling encodes information about the molecular dynamics in the nuclear spin self-relaxation and, more importantly, the electron/nuclear spin cross-relAXation rates.
Journal ArticleDOI
Heterogeneity in structure and dynamics of water near bilayers using TIP3P and TIP4P/2005 water models
TL;DR: In this article, the structure and dynamics of both lipids and water near membranes using simulations as in experiments is a challenging task, which is why it is difficult to capture structure and dynamic properties of both lipid and water.
Journal ArticleDOI
Microcirculatory Response to Photobiomodulation-Why Some Respond and Others Do Not: A Randomized Controlled Study
Lilach Gavish,Oshrit Hoffer,Neta Rabin,Neta Rabin,Moshe Halak,Simon Shkilevich,Yuval Shayovitz,Gal Weizman,Ortal Haim,Benjamin Gavish,S. David Gertz,Zehava Ovadia-Blechman +11 more
TL;DR: Investigation of factors affecting this patient‐specific response to photobiomodulation using advanced, noninvasive methods for monitoring microcirculatory activity found some individuals respond to PBM, but others do not.
Journal ArticleDOI
New insights on the mechanism of polyethylenimine transfection and their implications on gene therapy and DNA vaccines
TL;DR: In this article , the authors tracked the cell internalization of polyethylenimine (PEI) upon transfection to human epithelial cells and studied the interaction of PEI with phospholipidic layers mimicking nuclear membranes.
References
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Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Journal ArticleDOI
Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Journal ArticleDOI
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
Journal ArticleDOI
A smooth particle mesh Ewald method
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Journal ArticleDOI
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
TL;DR: A new implementation of the molecular simulation toolkit GROMACS is presented which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines.