scholarly journals On the Consistency of the Exfoliation Free Energy of Graphenes by Molecular Simulations

2021 ◽  
Vol 22 (15) ◽  
pp. 8291
Author(s):  
Anastasios Gotzias ◽  
Elena Tocci ◽  
Andreas Sapalidis
Keyword(s):  
Free Energy ◽  
Saline Water ◽  
Bilayer Graphene ◽  
Umbrella Sampling ◽  
Van Der Waals Interactions ◽  
Monolayer Graphene ◽  
Graphene Monolayer ◽  
Shear Direction ◽  
Liquid Environment ◽  
Before And After

Monolayer graphene is now produced at significant yields, by liquid phase exfoliation of graphites in solvents. This has increased the interest in molecular simulation studies to give new insights in the field. We use decoupling simulations to compute the exfoliation free energy of graphenes in a liquid environment. Starting from a bilayer graphene configuration, we decouple the Van der Waals interactions of a graphene monolayer in the presence of saline water. Then, we introduce the monolayer back into water by coupling its interactions with water molecules and ions. A different approach to compute the graphene exfoliation free energy is to use umbrella sampling. We apply umbrella sampling after pulling the graphene monolayer on the shear direction up to a distance from a bilayer. We show that the decoupling and umbrella methods give highly consistent free energy results for three bilayer graphene samples with different size. This strongly suggests that the systems in both methods remain closely in equilibrium as we move between the states before and after the exfoliation. Therefore, the amount of nonequilibrium work needed to peel the two layers apart is minimized efficiently.

scholarly journals Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase

2021 ◽  
Vol 118 (40) ◽  
pp. e2105507118
Author(s):  
Chigusa Kobayashi ◽  
Yasuhiro Matsunaga ◽  
Jaewoon Jung ◽  
Yuji Sugita
Keyword(s):  
Free Energy ◽  
Structural Changes ◽  
Umbrella Sampling ◽  
X Ray Crystallography ◽  
Atomic Structures ◽  
Energy Profiles ◽  
Intermediate States ◽  
Before And After ◽  
Energetic Analysis ◽  
Dynamics Simulations

Sarcoplasmic reticulum (SR) Ca2+-ATPase transports two Ca2+ ions from the cytoplasm to the SR lumen against a large concentration gradient. X-ray crystallography has revealed the atomic structures of the protein before and after the dissociation of Ca2+, while biochemical studies have suggested the existence of intermediate states in the transition between E1P⋅ADP⋅2Ca2+ and E2P. Here, we explore the pathway and free energy profile of the transition using atomistic molecular dynamics simulations with the mean-force string method and umbrella sampling. The simulations suggest that a series of structural changes accompany the ordered dissociation of ADP, the A-domain rotation, and the rearrangement of the transmembrane (TM) helices. The luminal gate then opens to release Ca2+ ions toward the SR lumen. Intermediate structures on the pathway are stabilized by transient sidechain interactions between the A- and P-domains. Lipid molecules between TM helices play a key role in the stabilization. Free energy profiles of the transition assuming different protonation states suggest rapid exchanges between Ca2+ ions and protons when the Ca2+ ions are released toward the SR lumen.

Numerical Analysis of Circular Graphene Bubbles

2013 ◽  
Vol 80 (4) ◽  
Author(s):  
Peng Wang ◽  
Wei Gao ◽  
Zhiyi Cao ◽  
Kenneth M. Liechti ◽  
Rui Huang
Keyword(s):  
Large Scale ◽  
Plate Theory ◽  
Approximate Solutions ◽  
Van Der Waals Interactions ◽  
Monolayer Graphene ◽  
Graphene Monolayer ◽  
Lateral Loads ◽  
Adhesive Properties ◽  
Dynamics Simulations ◽  
Low Pressures

Pressurized graphene bubbles have been observed in experiments, which can be used to determine the mechanical and adhesive properties of graphene. A nonlinear plate theory is adapted to describe the deformation of a graphene monolayer subject to lateral loads, where the bending moduli of monolayer graphene are independent of the in-plane Young's modulus and Poisson's ratio. A numerical method is developed to solve the nonlinear equations for circular graphene bubbles, and the results are compared to approximate solutions by analytical methods. Molecular dynamics simulations of nanoscale graphene bubbles are performed, and it is found that the continuum plate theory is suitable only within the limit of linear elasticity. Moreover, the effect of van der Waals interactions between graphene and its underlying substrate is analyzed, including large-scale interaction for nanoscale graphene bubbles subject to relatively low pressures.

scholarly journals A Novel Graphene Modelling: Bottom up Approach - Band Gap Studies to Transport in Python

2021 ◽  
Author(s):  
Bhavya Bhardwaj ◽  
Bala Tripura Sundari B
Keyword(s):  
Band Gap ◽  
Bilayer Graphene ◽  
Graphene Nanoribbon ◽  
Monolayer Graphene ◽  
Hamiltonian Matrix ◽  
Graphene Monolayer ◽  
Matrix Formulation ◽  
Material Models ◽  
Bottom Up ◽  
20 Nm

Abstract In this work we develop a computational, quantum level monolayer graphene nanoribbon (GNR) MOSFET of channel length of 10 and 20 nm, with a width of 2 nm and contacts of 2nm width is attached. To develop the MOSFET channel, a bottom up approach is adopted by developing the material model. First the material models of graphene nanoribbon is developed using pybinding module tool in python. The material models of monolayer, bilayer graphene nanoribbon are built on the principles of tight binding module. The methodology developed is based on the Hamiltonian matrix formulation that has been used to determine the E-k plots and LDOS plots of graphene monolayer, bilayer graphene nano ribbon. The GNR MOSFET that is structurally built in python is used to simulate graphene as a switch. Its band gap characteristics is presented as its performance as a switch and is verified with relevant work. Then GNR MOSFET is modelled using quantum principles of NEGF and greens function to determine the transmission characteristics and the I-V characteristics for channel lengths of 10 nm and 20 nm.

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

Nucleation free-energy barriers with Hybrid Monte-Carlo/Umbrella Sampling

2014 ◽  
Vol 16 (45) ◽  
pp. 24913-24919 ◽  
Author(s):  
M. A. Gonzalez ◽  
E. Sanz ◽  
C. McBride ◽  
J. L. F. Abascal ◽  
C. Vega ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Umbrella Sampling ◽  
Energy Barriers ◽  
Hybrid Monte Carlo

scholarly journals Free energy landscape for the entire transport cycle of triose-phosphate/phosphate translocator

2017 ◽  
Author(s):  
Mizuki Takemoto ◽  
Yongchan Lee ◽  
Ryuichiro Ishitani ◽  
Osamu Nureki
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Conformational Transition ◽  
Substrate Binding ◽  
Energy Landscape ◽  
Umbrella Sampling ◽  
Free Energy Landscape ◽  
Coupling Mechanism ◽  
Triose Phosphate ◽  
Phosphate Translocator

AbstractSecondary active transporters translocate their substrates using the electrochemical potentials of other chemicals, undergoing large-scale conformational changes. Despite extensive structural studies, the atomic details of the transport mechanism still remain elusive. Here we performed a series of all-atom molecular dynamics simulations of the triose-phosphate/phosphate translocator (TPT), which exports organic phosphates in the chloroplast stroma in strict counter exchange with inorganic phosphate (Pi). Biased sampling methods, including string method and umbrella sampling, successfully reproduced the conformational changes between the inward– and outward-facing states, along with the substrate binding. The free energy landscape of this entire TPT transition pathway demonstrated the alternating access and substrate translocation mechanisms, which revealed Pi is relayed by positively charged residues along the transition pathway. Furthermore, the conserved Glu207 functions as a “molecular switch”, linking the local substrate binding and the global conformational transition. Our results provide atomic-detailed insights into the energy coupling mechanism of antiporter.

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking

2015 ◽  
Vol 36 (20) ◽  
pp. 1489-1501 ◽  
Author(s):  
Junichi Higo ◽  
Bhaskar Dasgupta ◽  
Tadaaki Mashimo ◽  
Kota Kasahara ◽  
Yoshifumi Fukunishi ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Energy Landscape ◽  
Umbrella Sampling ◽  
Free Energy Landscape ◽  
Virtual System

scholarly journals Study of the Adhesion Mechanism of Acidithiobacillus ferrooxidans to Pyrite in Fresh and Saline Water

Minerals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 306 ◽  
Author(s):  
Francisca San Martín ◽  
Claudio Aguilar
Keyword(s):  
Fresh Water ◽  
Electrostatic Interactions ◽  
Saline Water ◽  
Streaming Potential ◽  
Bacterial Attachment ◽  
Van Der Waals Interactions ◽  
Streaming Potentials ◽  
Ph Values ◽  
Na Ions ◽  
Kinetics Of

In the present work, the streaming potential of A. ferrooxidans and pyrite was measured in two environments: fresh and saline water (water with 35 g/L of NaCl) at different pH values. Also, attachment kinetics of A. ferrooxidans to pyrite was studied in fresh and saline water at pH 4. The results show that A. ferrooxidans and pyrite had lower streaming potentials (comparing absolute values) in saline water than in fresh water, indicating the compression in the electrical double layer caused by Cl− and Na+ ions. It was also determined that the bacteria had a higher level of attachment to pyrite in fresh water than in saline water. The high ionic strength of saline water reduced the attractive force between A. ferrooxidans and pyrite, which in turn reduced bacterial attachment. Electrostatic interactions were determined to be mainly repulsive, since the bacteria and mineral had the same charge at pH 4. Despite this, the bacteria adhered to pyrite, indicating that hydrophobic attraction forces and Lifshitz–van der Waals interactions were stronger than electrostatic interactions, which caused the adhesion of A. ferrooxidans to pyrite.

Sign in / Sign up

Export Citation Format

Share Document