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Wilfred F Van Gunsteren - One of the best experts on this subject based on the ideXlab platform.

  • using enveloping distribution sampling to compute the folding free enthalpy of a β peptide with a very unstable folded conformation in solution the advantage of focused sampling using eds
    Chemical Physics, 2014
    Co-Authors: Zhixiong Lin, Ciprian Necula, Wilfred F Van Gunsteren
    Abstract:

    Abstract A peptide or a protein adopts a dynamic ensemble of conformations rather than a single structure in solution, although this ensemble may be dominated by one or a few particular folds. Computer simulation can be used to simulate the folding equilibria of peptides from which free Energy differences between different conformations can be calculated. However, standard molecular dynamics (MD) simulation is rather inefficient when the relative free Energy of a rather unstable fold is to be calculated. Here, we show, using a hepta-β-peptide with a very unstable 3 14 -helical conformation as an example, that the method of enveloping distribution sampling (EDS) offers a much more efficient alternative to compute the relative free Energy of different folds. The folding free energies obtained using the EDS method are compared with those obtained from three other methods: a standard MD simulation, from reweighting trajectories generated using hydrogen-bond restraints as umbrella Potential Energy Term to enhance the sampling of a particular fold, and from one-step perturbation. The EDS method yields the widest sampling of relevant conformations and shows the fastest convergence.

  • on searching in sampling of and dynamically moving through conformational space of biomolecular systems a review
    Journal of Computational Chemistry, 2008
    Co-Authors: Markus Christen, Wilfred F Van Gunsteren
    Abstract:

    Methods to search for low-Energy conformations, to generate a Boltzmann-weighted ensemble of configurations, or to generate classical-dynamical trajectories for molecular systems in the condensed liquid phase are briefly reviewed with an eye to application to biomolecular systems. After having chosen the degrees of freedom and method to generate molecular configurations, the efficiency of the search or sampling can be enhanced in various ways: (i) efficient calculation of the Energy function and forces, (ii) application of a plethora of search enhancement techniques, (iii) use of a biasing Potential Energy Term, and (iv) guiding the sampling using a reaction or transition pathway. The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Forbes, Richard G. - One of the best experts on this subject based on the ideXlab platform.

  • Comments on the continuing widespread and unnecessary use of a defective emission equation in field emission related literature
    'AIP Publishing', 2019
    Co-Authors: Forbes, Richard G.
    Abstract:

    Field electron emission (FE) has relevance in many different technological contexts. However, many related technological papers use a physically defective elementary FE equation for local emission current density (LECD). This equation takes the tunneling barrier as exactly triangular, as in the original FE theory of 90 years ago. More than 60 years ago, it was shown that the so-called Schottky-Nordheim (SN) barrier, which includes an image-Potential-Energy Term (that models exchange-and-correlation effects) is better physics. For a metal-like emitter with work-function 4.5 eV, the SN-barrier-related Murphy-Good FE equation predicts LECD values that are higher than the elementary equation values by a large factor, often between around 250 and around 500. By failing to mention/apply this 60-year-old established science, or to inform readers of the large errors associated with the elementary equation, many papers (aided by defective reviewing) spread a new kind of "pathological science", and create a modern research-integrity problem. The present paper aims to enhance author and reviewer awareness by summarizing relevant aspects of FE theory, by explicitly identifying the misjudgment in the original 1928 Fowler-Nordheim paper, by explicitly calculating the size of the resulting error, and by showing in detail why most FE theoreticians regard the 1950s modifications as better physics. Suggestions are made, about nomenclature and about citation practice, that may help to diminish misunderstandings.Comment: Submitted for publication; in v2 a correction to historical information (with no numerical consequences) has been made in Appendix

  • Comments on the continuing widespread and unnecessary use of a defective emission equation in field emission related literature
    'AIP Publishing', 2019
    Co-Authors: Forbes, Richard G.
    Abstract:

    Field electron emission (FE) has relevance in many technological contexts. However, many technological papers use a physically defective elementary FE equation for local emission current density (LECD). This equation takes the tunneling barrier as exactly triangular, as in the original FE theory of 90 years ago. More than 60 years ago, it was shown that the Schottky-Nordheim (SN) barrier, which includes an image-Potential-Energy Term (that models exchange-and-correlation effects) is better physics. For a metal-like emitter with work-function 4.5 eV, the SN-barrier-related Murphy-Good FE equation predicts LECD values that are higher than the elementary equation values by a large factor, often between 250 and 500. By failing to mention/apply this 60-year-old established science, or to inform readers of the large errors associated with the elementary equation, many papers (aided by inadequate reviewing) spread a new kind of "pathological science", and create a modern research-integrity problem. The present paper aims to enhance author and reviewer awareness by summarizing relevant aspects of FE theory, by explicitly identifying the misjudgment in the original 1928 Fowler-Nordheim paper, by explicitly calculating the size of the resulting error, and by showing in detail why most FE theoreticians regard the 1950s modifications as better physics. Suggestions are made, about nomenclature and about citation practice, that may help diminish misunderstandings. It is emphasized that the correction recommended here is one of several needed to improve the presentation of theory in FE literature, and only a first step towards higher-quality emission theory and improved methodology for current-voltage data interpretation

Ruggero Caminiti - One of the best experts on this subject based on the ideXlab platform.

  • the interpretation of diffraction patterns of two prototypical protic ionic liquids a challenging task for classical molecular dynamics simulations
    Journal of Physical Chemistry B, 2012
    Co-Authors: Lorenzo Gontrani, E Bodo, Alessandro Triolo, Francesca Leonelli, Paola Dangelo, Valentina Migliorati, Ruggero Caminiti
    Abstract:

    In this study, we discuss the performance of classical molecular dynamics in predicting the experimental X-ray diffraction patterns of liquid ethylammonium nitrate (one of the simplest protic room-temperature ionic liquid showing amphiphilic behavior) and of its hydroxy derivative (2-ethanolammonium nitrate, 2-HOEAN). Newly recorded Energy-dispersive X-ray diffraction structure factors are compared with the corresponding quantities extracted from molecular dynamics simulations. Other useful theoretical and experimental indicators are used as a probe of the local structure of the title ionic liquids. We shall show that the use of a general purpose, two-body Terms only, force field, such as OPLS/AA is able to describe most of the structural experimental data. However, we shall also point out that an improved description of some key structural features observed in the X-ray radial distribution function, can be obtained very easily by adding a general three-body Potential Energy Term instead of changing the t...

Hardik P Trivedi - One of the best experts on this subject based on the ideXlab platform.

  • an analytical study of Potential Energy Term in variablemoment of inertia nuclear softness mins model
    Advances in Applied Science Research, 2012
    Co-Authors: Hardik P Trivedi, Pallavi Bhatt, Anil Kumar, Lalit K Gupta, Jai Prakash Gupta, Than Singh Saini, Archna Kansal
    Abstract:

    In this paper, we have calculated Potential Energy Term in variable moment of inertia nuclear softness which shows the variation of Potential Energy Term for the different even-even nuclei in the region of I-quadrant based on the valence particle and hole pairs consideration [8]{Ce (N=90), Nd (N=92), Dy (N=92) & Dy (N-94)} with spin (J). The value of Potential Energy Term is increasing almost linear with increasing spin (J) for all the nuclei.

  • study of Potential Energy Term in vmins model
    DAE Symp.Nucl.Phys., 2012
    Co-Authors: Pallavi Bhatt, Anil Kumar, Lalit K Gupta, Jai Prakash Gupta, Than Singh Saini, Krishna Chandra, Hardik P Trivedi
    Abstract:

    Department of Physics, Mewar University, Chittorgarh (Rajasthan) INDIA, Department of Physics, Krishna Engineering College, Ghaziabad, INDIA Department of Physics, Vivekanand College of Tech. & Magt. Aligarh (UP) INDIA Department of Physics, Delhi Technological University, Delhi-42 INDIA Department of Physics, Goldfield institute of Technology & Management, Faridabad-, INDIA Department of Physics, D. S. College, Aligarh (UP), INDIA anil_kgupta@rediffmail.com

Lorenzo Gontrani - One of the best experts on this subject based on the ideXlab platform.

  • the interpretation of diffraction patterns of two prototypical protic ionic liquids a challenging task for classical molecular dynamics simulations
    Journal of Physical Chemistry B, 2012
    Co-Authors: Lorenzo Gontrani, E Bodo, Alessandro Triolo, Francesca Leonelli, Paola Dangelo, Valentina Migliorati, Ruggero Caminiti
    Abstract:

    In this study, we discuss the performance of classical molecular dynamics in predicting the experimental X-ray diffraction patterns of liquid ethylammonium nitrate (one of the simplest protic room-temperature ionic liquid showing amphiphilic behavior) and of its hydroxy derivative (2-ethanolammonium nitrate, 2-HOEAN). Newly recorded Energy-dispersive X-ray diffraction structure factors are compared with the corresponding quantities extracted from molecular dynamics simulations. Other useful theoretical and experimental indicators are used as a probe of the local structure of the title ionic liquids. We shall show that the use of a general purpose, two-body Terms only, force field, such as OPLS/AA is able to describe most of the structural experimental data. However, we shall also point out that an improved description of some key structural features observed in the X-ray radial distribution function, can be obtained very easily by adding a general three-body Potential Energy Term instead of changing the t...