BAR-based multi-dimensional nonequilibrium pulling for indirect construction of a QM/MM free energy landscape

2019 ◽  
Vol 21 (12) ◽  
pp. 6672-6688 ◽  
Author(s):  
Xiaohui Wang ◽  
Qiaole He ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Energy Landscapes ◽  
Free Energy Landscapes

Construction of free energy landscapes at the quantum mechanics (QM) level is computationally demanding.

Statistical analysis of vesicle morphology dynamics based on a free energy landscape

Soft Matter ◽  
2014 ◽  
Vol 10 (32) ◽  
pp. 6038-6046 ◽  
Author(s):  
Soichiro Tsuda ◽  
Hiroaki Suzuki ◽  
Tetsuya Yomo
Keyword(s):  
Free Energy ◽  
Statistical Analysis ◽  
Energy Landscape ◽  
Lipid Vesicles ◽  
Free Energy Landscape ◽  
Energy Landscapes ◽  
Microscope Images ◽  
Free Energy Landscapes

We here present a method to reconstruct effective free energy landscapes (FELs) of lipid vesicles from the statistical analysis of a large number of microscope images.

scholarly journals Universal free-energy landscape produces efficient and reversible electron bifurcation

2020 ◽  
Vol 117 (35) ◽  
pp. 21045-21051
Author(s):  
J. L. Yuly ◽  
P. Zhang ◽  
C. E. Lubner ◽  
J. W. Peters ◽  
D. N. Beratan
Keyword(s):  
Free Energy ◽  
Rate Constants ◽  
High Efficiency ◽  
Driving Forces ◽  
Energy Landscape ◽  
Molecular Machines ◽  
Free Energy Landscape ◽  
Energy Landscapes ◽  
Biological Catalysis ◽  
Free Energy Landscapes

For decades, it was unknown how electron-bifurcating systems in nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron-bifurcating molecular machines could not be designed and built. The underpinning free-energy landscapes for electron bifurcation were also enigmatic. We predict that a simple and universal free-energy landscape enables electron bifurcation, and we show that it enables high-efficiency bifurcation with limited short-circuiting (the EB scheme). The landscape relies on steep free-energy slopes in the two redox branches to insulate against short-circuiting using an electron occupancy blockade effect, without relying on nuanced changes in the microscopic rate constants for the short-circuiting reactions. The EB scheme thus unifies a body of observations on biological catalysis and energy conversion, and the scheme provides a blueprint to guide future campaigns to establish synthetic electron bifurcation machines.

scholarly journals GLASS TRANSITION TEMPERATURE AND FRACTAL DIMENSION OF PROTEIN FREE ENERGY LANDSCAPES

2000 ◽  
Vol 11 (02) ◽  
pp. 301-308 ◽  
Author(s):  
NELSON A. ALVES ◽  
ULRICH H. E. HANSMANN
Keyword(s):  
Free Energy ◽  
Fractal Dimension ◽  
Glass Transition ◽  
Transition Temperature ◽  
Glass Transition Temperature ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Energy Landscapes ◽  
Free Energy Landscapes

The free-energy landscape of two peptides is evaluated at various temperatures and an estimate for its fractal dimension at these temperatures calculated. We show that monitoring this quantity as a function of temperature allows to determine the glass transition temperature.

scholarly journals The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases

2015 ◽  
Vol 6 (2) ◽  
pp. 1167-1177 ◽  
Author(s):  
Javier Iglesias-Fernández ◽  
Lluís Raich ◽  
Albert Ardèvol ◽  
Carme Rovira
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Dynamics Simulations ◽  
Conformational Free Energy

Ab initio conformational free energy landscapes, together with molecular dynamics simulations, enable to predict the catalytic itineraries of β-xylanase enzymes.

scholarly journals BAR-Based Multi-Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Qiaole He ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Thermodynamic Cycle ◽  
Simulation Method ◽  
Collective Variable ◽  
Energy Simulation ◽  
Energy Landscapes ◽  
One Dimensional ◽  
Free Energy Landscapes ◽  
Energy Simulations

<p>Construction of free energy landscapes at Quantum mechanics (QM) level is computationally demanding. As shown in previous studies, by employing an indirect scheme (i.e. constructing a thermodynamic cycle connecting QM states via an alchemical pathway), simulations are converged with much less computational burden. The indirect scheme makes QM/ molecular mechanics (MM) free energy simulation orders of magnitude faster than the direct QM/MM schemes. However, the indirect QM/MM simulations were mostly equilibrium sampling based and the nonequilibrium methods were merely exploited in one-dimensional alchemical QM/MM end-state correction at two end states. In this work, we represent a multi-dimensional nonequilibrium pulling scheme for indirect QM/MM free energy simulations, where the whole free energy simulation is performed only with nonequilibrium methods. The collective variable (CV) space we explore is a combination of one alchemical CV and one physically meaningful CV. The current nonequilibrium indirect QM/MM simulation method can be seen as the generalization of equilibrium perturbation based indirect QM/MM methods. The test systems include one backbone dihedral case and one distance case. The two cases are significantly different in size, enabling us to investigate the dependence of the speedup of the indirect scheme on the size of the system. It is shown that the speedup becomes larger when the size of the system becomes larger, which is consistent with the scaling behavior of QM Hamiltonians. </p>

BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM/MM free energy landscapes: from semi-empirical to ab initio

2019 ◽  
Vol 21 (39) ◽  
pp. 21942-21959 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Indirect Method ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Energy Simulations ◽  
Semi Empirical

The indirect method for the construction of quantum mechanics (QM)/molecular mechanics (MM) free energy landscapes provides a cheaper alternative for free energy simulations at the QM level.

scholarly journals BAR-Based Multi-Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscape

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Qiaole He ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Thermodynamic Cycle ◽  
Simulation Method ◽  
Collective Variable ◽  
Energy Simulation ◽  
Energy Landscapes ◽  
One Dimensional ◽  
Free Energy Landscapes ◽  
Energy Simulations

<p>Construction of free energy landscapes at Quantum mechanics (QM) level is computationally demanding. As shown in previous studies, by employing an indirect scheme (i.e. constructing a thermodynamic cycle connecting QM states via an alchemical pathway), simulations are converged with much less computational burden. The indirect scheme makes QM/ molecular mechanics (MM) free energy simulation orders of magnitude faster than the direct QM/MM schemes. However, the indirect QM/MM simulations were mostly equilibrium sampling based and the nonequilibrium methods were merely exploited in one-dimensional alchemical QM/MM end-state correction at two end states. In this work, we represent a multi-dimensional nonequilibrium pulling scheme for indirect QM/MM free energy simulations, where the whole free energy simulation is performed only with nonequilibrium methods. The collective variable (CV) space we explore is a combination of one alchemical CV and one physically meaningful CV. The current nonequilibrium indirect QM/MM simulation method can be seen as the generalization of equilibrium perturbation based indirect QM/MM methods. The test systems include one backbone dihedral case and one distance case. The two cases are significantly different in size, enabling us to investigate the dependence of the speedup of the indirect scheme on the size of the system. It is shown that the speedup becomes larger when the size of the system becomes larger, which is consistent with the scaling behavior of QM Hamiltonians. </p>

scholarly journals Sonifying Stochastic Walks on Biomolecular Energy Landscapes

2018 ◽  
Author(s):  
Robert E. Arbon ◽  
Alex J. Jones ◽  
Lars A. Bratholm ◽  
Tom Mitchell ◽  
David R. Glowacki
Keyword(s):  
Free Energy ◽  
Markov Models ◽  
Dynamic Properties ◽  
Energy Landscape ◽  
Visual Display ◽  
Free Energy Landscape ◽  
Auditory Display ◽  
Energy Landscapes ◽  
Biomolecular Systems ◽  
Relative Free Energy

Translating the complex, multi-dimensional data produced by simulations of biomolecules into an intelligible form is a major challenge in computational chemistry and biology. The so-called “free energy landscape” is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for mapping features of this landscape to sonic parameters, for use in conjunction with visual display techniques such as structural animations and free energy diagrams. This allows for concurrent visual display of the physical configuration of a biomolecule and auditory display of characteristics of the corresponding free energy landscape. The resulting sonification provides information about the relative free energy features of a given configuration including its stability.

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>

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