scholarly journals Bridging scales in disordered porous media by mapping molecular dynamics onto intermittent Brownian motion

2020 ◽  
Author(s):  
Colin Bousige ◽  
Pierre Levitz ◽  
Benoit Coasne
Keyword(s):  
Molecular Dynamics ◽  
Surface Heterogeneity ◽  
State Theory ◽  
Free Energy Barrier ◽  
Nanoporous Media ◽  
Strong Surface ◽  
Diffusion Mechanisms ◽  
The One ◽  
Physical Laws ◽  
Disordered Porous Media

Abstract Owing to their complex pore morphology and strong surface heterogeneity, disordered nanoporous media possess a rich underlying diffusion landscape that gives rise to specific transport phenomena. The unique diffusion mechanisms in such heterogeneous, ultra-confining solids stem from restricted pore relocation and blurred, i.e. ill-defined, pore/surface boundaries. As a result, while the fundamentals of diffusion and transport in simple pore geometries are well-established, the case of fluids confined in such complex porous materials still challenges existing frameworks. Here, we invoke the intermittent surface/pore diffusion formalism to map molecular dynamics onto random walk in disordered nanoporous media. Our hierarchical strategy allows quantitatively bridging microscopic and mesoscopic dynamics with parameters obtained from simple physical laws. In more detail, the surface residence and relocation times - t_A, t_B - are shown to derive from pore size p and temperature-rescaled surface interaction ε/k_BT. On the one hand, t_A obeys a transition state theory with an adsorption free energy barrier ~ε/k_BT and a prefactor ~1ps corrected for pore curvature p. On the other hand, t_B scales with p which is rationalized through a cutoff in the relocation first passage distribution. Beyond fundamental implications, the present approach provides a robust formalism to predict diffusion for any fluid in complex nanoporous media using fluid and material parameters available to simple experiments.

scholarly journals Bridging scales in disordered porous media by mapping molecular dynamics onto intermittent Brownian motion

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Colin Bousige ◽  
Pierre Levitz ◽  
Benoit Coasne
Keyword(s):  
Molecular Dynamics ◽  
Transition State Theory ◽  
Pore Diameter ◽  
State Theory ◽  
Complex Materials ◽  
Nanoporous Media ◽  
Complex Morphology ◽  
Diffusion Mechanisms ◽  
Disordered Porous Media ◽  
Fluid Diffusion

AbstractOwing to their complex morphology and surface, disordered nanoporous media possess a rich diffusion landscape leading to specific transport phenomena. The unique diffusion mechanisms in such solids stem from restricted pore relocation and ill-defined surface boundaries. While diffusion fundamentals in simple geometries are well-established, fluids in complex materials challenge existing frameworks. Here, we invoke the intermittent surface/pore diffusion formalism to map molecular dynamics onto random walk in disordered media. Our hierarchical strategy allows bridging microscopic/mesoscopic dynamics with parameters obtained from simple laws. The residence and relocation times – tA, tB – are shown to derive from pore size d and temperature-rescaled surface interaction ε/kBT. tA obeys a transition state theory with a barrier ~ε/kBT and a prefactor ~10−12 s corrected for pore diameter d. tB scales with d which is rationalized through a cutoff in the relocation first passage distribution. This approach provides a formalism to predict any fluid diffusion in complex media using parameters available to simple experiments.

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

scholarly journals OH− and H3O+ Diffusion in Model AEMs and PEMs at Low Hydration: Insights from Ab Initio Molecular Dynamics

Membranes ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 355
Author(s):  
Tamar Zelovich ◽  
Mark E. Tuckerman
Keyword(s):  
Molecular Dynamics ◽  
Fuel Cell ◽  
Ab Initio ◽  
Cost Effective ◽  
Clean Energy ◽  
Proton Exchange ◽  
Ab Initio Molecular Dynamics ◽  
Anion Exchange Membranes ◽  
Diffusion Mechanisms ◽  
Dynamics Simulations

Fuel cell-based anion-exchange membranes (AEMs) and proton exchange membranes (PEMs) are considered to have great potential as cost-effective, clean energy conversion devices. However, a fundamental atomistic understanding of the hydroxide and hydronium diffusion mechanisms in the AEM and PEM environment is an ongoing challenge. In this work, we aim to identify the fundamental atomistic steps governing hydroxide and hydronium transport phenomena. The motivation of this work lies in the fact that elucidating the key design differences between the hydroxide and hydronium diffusion mechanisms will play an important role in the discovery and determination of key design principles for the synthesis of new membrane materials with high ion conductivity for use in emerging fuel cell technologies. To this end, ab initio molecular dynamics simulations are presented to explore hydroxide and hydronium ion solvation complexes and diffusion mechanisms in the model AEM and PEM systems at low hydration in confined environments. We find that hydroxide diffusion in AEMs is mostly vehicular, while hydronium diffusion in model PEMs is structural. Furthermore, we find that the region between each pair of cations in AEMs creates a bottleneck for hydroxide diffusion, leading to a suppression of diffusivity, while the anions in PEMs become active participants in the hydronium diffusion, suggesting that the presence of the anions in model PEMs could potentially promote hydronium diffusion.

Substrate induced freezing, melting and depinning transitions in two-dimensional liquid crystalline systems

2022 ◽  
Author(s):  
Bharti bharti ◽  
Debabrata Deb
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystals ◽  
Molecular Dynamics Simulations ◽  
Liquid Crystalline ◽  
Two Dimensional ◽  
One Dimensional ◽  
The One ◽  
Dynamics Simulations

We use molecular dynamics simulations to investigate the ordering phenomena in two-dimensional (2D) liquid crystals over the one-dimensional periodic substrate (1DPS). We have used Gay-Berne (GB) potential to model the...

scholarly journals Compressing molecular dynamics trajectories: Breaking the one-bit-per-sample barrier

2016 ◽  
Vol 37 (20) ◽  
pp. 1897-1906 ◽  
Author(s):  
Jan Huwald ◽  
Stephan Richter ◽  
Bashar Ibrahim ◽  
Peter Dittrich
Keyword(s):  
Molecular Dynamics ◽  
The One

scholarly journals Analytical results in transient brush tyre models: theory for large camber angles and classic solutions with limited friction

Meccanica ◽  
2021 ◽  
Author(s):  
Luigi Romano ◽  
Francesco Timpone ◽  
Fredrik Bruzelius ◽  
Bengt Jacobson
Keyword(s):  
Rolling Direction ◽  
State Theory ◽  
General Situation ◽  
Linear Dynamical Systems ◽  
Transient Conditions ◽  
One Dimensional ◽  
Analytical Results ◽  
Classic Theory ◽  
Uniqueness Of The Solution ◽  
The One

AbstractThis paper establishes new analytical results in the mathematical theory of brush tyre models. In the first part, the exact problem which considers large camber angles is analysed from the perspective of linear dynamical systems. Under the assumption of vanishing sliding, the most salient properties of the model are discussed with some insights on concepts as existence and uniqueness of the solution. A comparison against the classic steady-state theory suggests that the latter represents a very good approximation even in case of large camber angles. Furthermore, in respect to the classic theory, the more general situation of limited friction is explored. It is demonstrated that, in transient conditions, exact sliding solutions can be determined for all the one-dimensional problems. For the case of pure lateral slip, the investigation is conducted under the assumption of a strictly concave pressure distribution in the rolling direction.

scholarly journals pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL

2018 ◽  
Vol 20 (5) ◽  
pp. 3523-3530 ◽  
Author(s):  
Zhi Yue ◽  
Jana Shen
Keyword(s):  
Molecular Dynamics ◽  
Energy Barrier ◽  
Molten Globule ◽  
Free Energy Barrier ◽  
Molten Globule State ◽  
Constant Ph ◽  
Ph Dependent ◽  
Dynamics Simulations ◽  
Constant Ph Molecular Dynamics ◽  
Folding Free Energy

Constant pH molecular dynamics simulations of BBL reveals negligible folding free energy barrier that is pH dependent and a sparsely populated dry molten globule state.

Freund-Feind-Denken

2021 ◽  
Keyword(s):  
Armed Forces ◽  
State Theory ◽  
Carl Schmitt ◽  
Professor Emeritus ◽  
The Political ◽  
Political Sphere ◽  
Relevant Today ◽  
German Armed Forces ◽  
The One ◽  
The University

Carl Schmitt emphasised the crucial importance of the friend–enemy dichotomy for the political sphere. Is the connection between the concept of the enemy and politics still relevant today? Or does the political sphere need to be defined quite differently, on the one hand, and does the problem of enmity need to be dealt with beyond the political sphere, on the other? Since the publication of this book’s 1st edition, the issue of ‘enmity’ has by no means been settled, as recent terrorist attacks have shown. On the contrary, hatred of those who think differently seems to be on the increase, and they are then demonised as ‘enemies’. This development is explored in the contributions to the book’s 2nd edition. Rüdiger Voigt, professor emeritus of administrative science at the University of the German Armed Forces in Munich, is the author and editor of numerous books on state theory and state practice.

Introduction

2003 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Computational Chemistry ◽  
Mathematical Theory ◽  
Fundamental Equation ◽  
Point Of View ◽  
Scaling Relations ◽  
Approximate Methods ◽  
Computational Speed ◽  
Diverse Field ◽  
Physical Laws

Molecular dynamics deals with the motion of and the reaction between atoms and molecules. The fundamental theory for the description of essentially all aspects of the area has been known and defined through the non-relativistic Schrdinger equation since 1926. The “only” problem, therefore, is the solution of this fundamental equation. Unfortunately, this solution is not straightforward and, as early as 1929, prompted the following remark by Dirac (1929). . . The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the application of these laws leads to equations much too complicated to be soluble. . . . Dirac could, for that matter, have added the area of molecular biochemistry. But here the systems become even bigger and therefore the above statement is even more correct. What neither Dirac nor anybody else at that time could foresee was the invention of the computer. With that, a whole new area, namely that of computational chemistry, was created. The recent five-volume work Encyclopedia of Computational Chemistry (1998[1]), with several hundred entries, bears witness to the tremendous evolution in this particular area over the last fifty years or so. The success of computational chemistry has to do not only with computers and the increase in computational speed but also with the development of new methods. Here again it should be emphasized that the availability of computers makes the construction of approximate methods a very rich and diverse field with many possibilities. Thus, this combination of computer power and the invention of theoretical and computational methods has changed the pessimistic point of view into an optimistic one. To quote Clementi (1972), “We can calculate everything.” Although this statement, at least in 1972, was somewhat optimistic, development since then has shown that the attitude should be quite optimistic. The purpose of approximate methods should be, and always is, to try to circumvent the bad scaling relations of quantum mechanics.

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