Universal Trend of the Non-Exponential Rouse Mode Relaxation in Glass-Forming Polymers Systems: Experimental Facts, MD-Simulation Results and a Theoretical Approach Based on a Generalized Langevin Equation

MRS Advances ◽  
2016 ◽  
Vol 1 (26) ◽  
pp. 1903-1913 ◽  
Author(s):  
J. Colmenero
Keyword(s):  
Langevin Equation ◽  
Theoretical Approach ◽  
Md Simulation ◽  
Memory Function ◽  
Md Simulations ◽  
Generalized Langevin Equation ◽  
Exponential Behavior ◽  
Glass Forming ◽  
Chain Stiffness ◽  
Local Potentials

ABSTRACTNowadays there are clear evidences from both experiments and MD-simulations proving that the chain Rouse modes correlation functions are non-exponential in unentangled polymer blends and also in pure polymers at low temperature (with respect to that of the glass transition Tg) even for the long wavelengths modes where local potentials and chain stiffness should not play any role. In a recent paper [S. Arrese-Igor et al, Phys. Rev. Lett.113, 078302 (2014)] it has been proposed that this non-exponential behavior depends on the ratio between the so-called Rouse time - i.e., the characteristic time of the slowest chain mode relaxation - and the time scale of the α-relaxation. This parameter is in some way ‘universal’ in the meaning that it can encode many different experimental situations. In this paper, we show that this behavior can be quantitatively explained in the framework of a theoretical approach based on: (i) a generalized Langevin equation (GLE) formalism and (ii) a memory function which takes into account the effect of collective dynamics on the chain dynamics of a tagged chain and which was constructed taking inspirations from the original ideas of the reptation model proposed by de Gennes.

scholarly journals Coupling between structural relaxation and diffusion in glass-forming liquids under pressure variation

2020 ◽  
Vol 22 (42) ◽  
pp. 24365-24371
Author(s):  
Anh D. Phan ◽  
Kajetan Koperwas ◽  
Marian Paluch ◽  
Katsunori Wakabayashi
Keyword(s):  
Molecular Dynamics ◽  
Langevin Equation ◽  
Structural Relaxation ◽  
Md Simulations ◽  
Pressure Variation ◽  
Glass Forming ◽  
Nonlinear Langevin Equation ◽  
And Diffusion

We theoretically investigate structural relaxation and activated diffusion of glass-forming liquids at different pressures using both Elastically Collective Nonlinear Langevin Equation (ECNLE) theory and molecular dynamics (MD) simulations.

A comprehensive in silico study towards understanding the inhibitory mechanism of Lactoperoxidase by Dapsone and Propofol

2020 ◽  
Vol 16 ◽  
Author(s):  
Rameez Jabeer Khan ◽  
Rajat Kumar Jha ◽  
Gizachew Muluneh Amera ◽  
Jayaraman Muthukumaran ◽  
Rashmi Prabha Singh ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Protoporphyrin Ix ◽  
Md Simulations ◽  
Prosthetic Group ◽  
Drug Molecules ◽  
Group A ◽  
Complex Forms ◽  
Covalently Linked

Introduction: Lactoperoxidase (LPO) is a member of mammalian heme peroxidase family and is an enzyme of innate immune system. It possesses a covalently linked heme prosthetic group (a derivative of protoporphyrin IX) in its active site. LPO catalyzes the oxidation of halides and pseudohalides in the presence of hydrogen peroxide (H2O2) and shows a broad range of antimicrobial activity. Methods: In this study, we have used two pharmaceutically important drug molecules, namely dapsone and propofol, which are earlier reported as potent inhibitors of LPO. Whereas the stereochemistry and mode of binding of dapsone and propofol to LPO is still not known because of the lack of the crystal structure of LPO with these two drugs. In order to fill this gap, we utilized molecular docking and molecular dynamics (MD) simulation studies of LPO in native and complex forms with dapsone and propofol. Results: From the docking results, the estimated binding free energy (ΔG) of -9.25 kcal/mol (Ki = 0.16 μM) and -7.05 kcal/mol (Ki = 6.79 μM) was observed for dapsone, and propofol, respectively. The standard error of Auto Dock program is 2.5 kcal/mol; therefore, molecular docking results alone were inconclusive. Conclusion: To further validate the docking results, we performed MD simulation on unbound, and two drugs bounded LPO structures. Interestingly, MD simulations results explained that the structural stability of LPO-Propofol complex was higher than LPO-Dapsone complex. The results obtained from this study establish the mode of binding and interaction pattern of the dapsone and propofol to LPO as inhibitors.

scholarly journals Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sensen Zhang ◽  
Baolei Yuan ◽  
Jordy Homing Lam ◽  
Jun Zhou ◽  
Xuan Zhou ◽  
...  
Keyword(s):  
Md Simulation ◽  
Potential Role ◽  
Md Simulations ◽  
Full Length ◽  
Inflammasome Activation ◽  
Simulation Studies ◽  
Cryo Electron Microscopy ◽  
Gating Mechanism ◽  
Atp Efflux

AbstractPannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.

scholarly journals Fully Atomistic Molecular Dynamics Computation of Physico-Mechanical Properties of PB, PS, and SBS

Nanomaterials ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 1088 ◽  
Author(s):  
Yang Kang ◽  
Dunhong Zhou ◽  
Qiang Wu ◽  
Fuyan Duan ◽  
Rufang Yao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Strain Rate ◽  
Strain Hardening ◽  
Md Simulation ◽  
Md Simulations ◽  
Strain Rates ◽  
Young’S Moduli ◽  
Plastic Modulus ◽  
Styrene Butadiene ◽  
Butadiene Styrene

The physical properties—including density, glass transition temperature (Tg), and tensile properties—of polybutadiene (PB), polystyrene (PS) and poly (styrene-butadiene-styrene: SBS) block copolymer were predicted by using atomistic molecular dynamics (MD) simulation. At 100 K, for PB and SBS under uniaxial tension with strain rate ε ˙ = 1010 s−1 and 109 s−1, their stress–strain curves had four features, i.e., elastic, yield, softening, and strain hardening. At 300 K, the tensile curves of the three polymers with strain rates between 108 s−1 and 1010 s−1 exhibited strain hardening following elastic regime. The values of Young’s moduli of the copolymers were independent of strain rate. The plastic modulus of PS was independent of strain rate, but the Young’s moduli of PB and SBS depended on strain rate under the same conditions. After extrapolating the Young’s moduli of PB and SBS at strain rates of 0.01–1 s−1 by the linearized Eyring-like model, the predicted results by MD simulations were in accordance well with experimental results, which demonstrate that MD results are feasible for design of new materials.

scholarly journals The study of dynamic singularities of seismic signals by the generalized Langevin equation

2009 ◽  
Vol 388 (17) ◽  
pp. 3629-3635 ◽  
Author(s):  
Renat Yulmetyev ◽  
Ramil Khusnutdinoff ◽  
Timur Tezel ◽  
Yildiz Iravul ◽  
Bekir Tuzel ◽  
...  
Keyword(s):  
Langevin Equation ◽  
Generalized Langevin Equation ◽  
Seismic Signals
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