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Josef Michl - One of the best experts on this subject based on the ideXlab platform.
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Friction in carborane based molecular rotors driven by gas flow or electric field classical molecular dynamics
ACS Nano, 2012Co-Authors: Alexandr Prokop, Jaroslav Vacek, Josef MichlAbstract:Friction in molecular rotors is examined by classical molecular dynamics simulations for grid-mounted azimuthal dipolar molecular rotors, whose rotation is either allowed to decay freely or is driven at GHz frequencies by a flow of rare gas or by a rotating electric field. The rotating parts (rotators) are propeller-shaped. Their two to six blades consist of condensed aromatic rings and are attached to a deltahedral carborane hub, whose antipodal carbons carry [n]staffane axles mounted on a square molecular grid. The dynamic Friction Constant η has been derived in several independent ways with similar results. Analysis of free rotation decay yields η as a continuous exponentially decreasing function of rotor frequency. The calculated dependence of Friction torque on frequency resembles the classical macroscopic Stribeck curve. Its relation to rotational potential energy barriers and the key role of the rate of intramolecular vibrational redistribution (IVR) of energy and angular momentum from rotator rota...
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molecular dynamics simulation of an electric field driven dipolar molecular rotor attached to a quartz glass surface
Journal of the American Chemical Society, 2003Co-Authors: Dominik Horinek, Josef MichlAbstract:Molecular dynamics simulations of the response of a dipolar azimuthal 3-chloroprop-1-ynyl rotor mounted on the surface of quartz glass to a rotating electric field were performed. The rotor motion was classified as synchronous, asynchronous, random, or hindered, based on the value of the average lag of the rotor behind the field and a comparison of the intrinsic rotational barrier Vb with kT. A phase diagram of rotor behavior was deduced at 10, 300, and 500 K as a function of field strength and frequency. A simple model for the rotor motion was developed, containing the driving force, the temperature, the height of the torsional barrier, and the Friction Constant of the rotor. Defining Ebo to be the electric field strength necessary to get rotational response from the rotor (“breakoff field”) and μ to be the rotor dipole moment component in the plane of rotation, we find that Ebo is frequency independent when 2μEbo is less than either Vb or kT (the driving force needs to overcome the more important of the...
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molecular dynamics of a grid mounted molecular dipolar rotor in a rotating electric field
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Jaroslav Vacek, Josef MichlAbstract:Abstract Classical molecular dynamics is applied to the rotation of a dipolar molecular rotor mounted on a square grid and driven by rotating electric field E(ν) at T ≃ 150 K. The rotor is a complex of Re with two substituted o-phenanthrolines, one positively and one negatively charged, attached to an axial position of Rh in a [2]staffanedicarboxylate grid through 2-(3-cyanobicyclo[1.1.1]pent-1-yl)malonic dialdehyde. Four regimes are characterized by a, the average lag per turn: (i) synchronous (a Ec(ν) [Ec(ν) is the critical field strength], (ii) asynchronous (1/e E(ν) > Ebo(ν) > kT/μ, [Ebo(ν) is the break-off field strength], (iii) random driven (a ≃ 1) at Ebo(ν) > E(ν) > kT/μ, and (iv) random thermal (a ≃ 1) at kT/μ > E(ν). A fifth regime, (v) strongly hindered, W > kT, Eμ, (W is the rotational barrier), has not been examined. We find Ebo(ν)/kVcm−1 ≃ (kT/μ)/kVcm−1 + 0.13(ν/GHz)1.9 and Ec(ν)/kVcm−1 ≃ (2.3kT/μ)/kVcm−1 + 0.87(ν/GHz)1.6. For ν > 40 GHz, the rotor behaves as a macroscopic body with a Friction Constant proportional to frequency, η/eVps ≃ 1.14 ν/THz, and for ν < 20 GHz, it exhibits a uniquely molecular behavior.
Jaroslav Vacek - One of the best experts on this subject based on the ideXlab platform.
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Friction in carborane based molecular rotors driven by gas flow or electric field classical molecular dynamics
ACS Nano, 2012Co-Authors: Alexandr Prokop, Jaroslav Vacek, Josef MichlAbstract:Friction in molecular rotors is examined by classical molecular dynamics simulations for grid-mounted azimuthal dipolar molecular rotors, whose rotation is either allowed to decay freely or is driven at GHz frequencies by a flow of rare gas or by a rotating electric field. The rotating parts (rotators) are propeller-shaped. Their two to six blades consist of condensed aromatic rings and are attached to a deltahedral carborane hub, whose antipodal carbons carry [n]staffane axles mounted on a square molecular grid. The dynamic Friction Constant η has been derived in several independent ways with similar results. Analysis of free rotation decay yields η as a continuous exponentially decreasing function of rotor frequency. The calculated dependence of Friction torque on frequency resembles the classical macroscopic Stribeck curve. Its relation to rotational potential energy barriers and the key role of the rate of intramolecular vibrational redistribution (IVR) of energy and angular momentum from rotator rota...
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molecular dynamics of a grid mounted molecular dipolar rotor in a rotating electric field
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Jaroslav Vacek, Josef MichlAbstract:Abstract Classical molecular dynamics is applied to the rotation of a dipolar molecular rotor mounted on a square grid and driven by rotating electric field E(ν) at T ≃ 150 K. The rotor is a complex of Re with two substituted o-phenanthrolines, one positively and one negatively charged, attached to an axial position of Rh in a [2]staffanedicarboxylate grid through 2-(3-cyanobicyclo[1.1.1]pent-1-yl)malonic dialdehyde. Four regimes are characterized by a, the average lag per turn: (i) synchronous (a Ec(ν) [Ec(ν) is the critical field strength], (ii) asynchronous (1/e E(ν) > Ebo(ν) > kT/μ, [Ebo(ν) is the break-off field strength], (iii) random driven (a ≃ 1) at Ebo(ν) > E(ν) > kT/μ, and (iv) random thermal (a ≃ 1) at kT/μ > E(ν). A fifth regime, (v) strongly hindered, W > kT, Eμ, (W is the rotational barrier), has not been examined. We find Ebo(ν)/kVcm−1 ≃ (kT/μ)/kVcm−1 + 0.13(ν/GHz)1.9 and Ec(ν)/kVcm−1 ≃ (2.3kT/μ)/kVcm−1 + 0.87(ν/GHz)1.6. For ν > 40 GHz, the rotor behaves as a macroscopic body with a Friction Constant proportional to frequency, η/eVps ≃ 1.14 ν/THz, and for ν < 20 GHz, it exhibits a uniquely molecular behavior.
Ambjornsson Tobias - One of the best experts on this subject based on the ideXlab platform.
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Stochastic unfolding of nanoconfined DNA: experiments, model and Bayesian analysis
'AIP Publishing', 2020Co-Authors: Krog Jens, Alizadehheidari Mohammadreza, Werner Erik, Bikkarolla, Santosh Kumar, Tegenfeldt, Jonas O., Mehlig Bernhard, Lomholt, Michael A., Westerlund Fredrik, Ambjornsson TobiasAbstract:Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force as well as the Friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the Friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory type argument. The estimated Friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated Friction Constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement.Comment: 21 pages, 8 figure
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Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis
'AIP Publishing', 2018Co-Authors: Krog Jens, Alizadehheidari Mohammadreza, Werner Erik, Tegenfeldt, Jonas O., Mehlig Bernhard, Lomholt, Michael A., Westerlund Fredrik, Kumar Bikarolla Santosh, Ambjornsson TobiasAbstract:Nanochannels provide a means for detailed experiments on the effect of confinement on biomacro-molecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the Friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the Friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated Friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated Friction Constant by extracting this parameter from DNA\u27s center-of -mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis. Published by AIP Publishing
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Stochastic unfolding of nanoconfined DNA : Experiments, model and Bayesian analysis
'AIP Publishing', 2018Co-Authors: Krog Jens, Alizadehheidari Mohammadreza, Werner Erik, Bikkarolla, Santosh Kumar, Tegenfeldt, Jonas O., Mehlig Bernhard, Lomholt, Michael A., Westerlund Fredrik, Ambjornsson TobiasAbstract:Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the Friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the Friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated Friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated Friction Constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis
Alexandr Prokop - One of the best experts on this subject based on the ideXlab platform.
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Friction in carborane based molecular rotors driven by gas flow or electric field classical molecular dynamics
ACS Nano, 2012Co-Authors: Alexandr Prokop, Jaroslav Vacek, Josef MichlAbstract:Friction in molecular rotors is examined by classical molecular dynamics simulations for grid-mounted azimuthal dipolar molecular rotors, whose rotation is either allowed to decay freely or is driven at GHz frequencies by a flow of rare gas or by a rotating electric field. The rotating parts (rotators) are propeller-shaped. Their two to six blades consist of condensed aromatic rings and are attached to a deltahedral carborane hub, whose antipodal carbons carry [n]staffane axles mounted on a square molecular grid. The dynamic Friction Constant η has been derived in several independent ways with similar results. Analysis of free rotation decay yields η as a continuous exponentially decreasing function of rotor frequency. The calculated dependence of Friction torque on frequency resembles the classical macroscopic Stribeck curve. Its relation to rotational potential energy barriers and the key role of the rate of intramolecular vibrational redistribution (IVR) of energy and angular momentum from rotator rota...
Alexander M Berezhkovskii - One of the best experts on this subject based on the ideXlab platform.
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time scale separation leads to position dependent diffusion along a slow coordinate
Journal of Chemical Physics, 2011Co-Authors: Alexander M Berezhkovskii, Attila SzaboAbstract:When there is a separation of time scales, an effective description of the dynamics of the slow variables can be obtained by adiabatic elimination of fast ones. For example, for anisotropic Langevin dynamics in two dimensions, the conventional procedure leads to a Langevin equation for the slow coordinate that involves the potential of the mean force. The Friction Constant along this coordinate remains unchanged. Here, we show that a more accurate, but still Markovian, description of the slow dynamics can be obtained by using position-dependent Friction that is related to the time integral of the autocorrelation function of the difference between the actual force and the mean force by a Kirkwood-like formula. The result is generalized to many dimensions, where the slow or reaction coordinate is an arbitrary function of the Cartesian coordinates. When the fast variables are effectively one-dimensional, the additional Friction along the slow coordinate can be expressed in closed form for an arbitrary potential. For a cylindrically symmetric channel of varying cross section with winding centerline, our analytical expression immediately yields the multidimensional version of the Zwanzig-Bradley formula for the position-dependent diffusion coefficient.
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escape from a cavity through a small window turnover of the rate as a function of Friction Constant
Journal of Chemical Physics, 2006Co-Authors: Alexander M Berezhkovskii, Yurii A Makhnovskii, Vladimir Yu ZitsermanAbstract:To escape from a cavity through a small window the particle has to overcome a high entropy barrier to find the exit. As a consequence, its survival probability in the cavity decays as a single exponential and is characterized by the only parameter, the rate Constant. We use simulations to study escape of Langevin particles from a cubic cavity through a small round window in the center of one of the cavity walls with the goal of analyzing the Friction dependence of the escape rate. We find that the rate Constant shows the turnover behavior as a function of the Friction Constant, ζ: The rate Constant grows at very small ζ, reaches a maximum value which is given by the transition-state theory (TST), and then decreases approaching zero as ζ→∞. Based on the results found in simulations and some general arguments we suggest a formula for the rate Constant that predicts a turnover of the escape rate for ergodic cavities in which collisions of the particle with the cavity walls are defocusing. At intermediate-to-...
