Accelerating convergence of molecular dynamics-based structural relaxation
Christensen, Asbjørn
2005-01-01
We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...
Accelerating convergence of molecular dynamics-based structural relaxation
Christensen, Asbjørn
2005-01-01
We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...... efficiency. We also discuss the implementation aspects. Secondly, we explore the final state refinement acceleration by a combination with the conjugate gradient technique, where the key ingredient is an implicit corrector step. Finally, we test the feasibility of passive Hessian matrix accumulation from...
Excitation dynamics and relaxation in a molecular heterodimer
Balevicius, V.; Gelzinis, A. [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Avenue 9, build. 3, LT-10222 Vilnius (Lithuania); Center for Physical Sciences and Technology, Institute of Physics, Savanoriu Avenue 231, LT-02300 Vilnius (Lithuania); Abramavicius, D. [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Avenue 9, build. 3, LT-10222 Vilnius (Lithuania); State Key Laboratory of Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Street, Changchun 130012 (China); Mancal, T. [Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2 (Czech Republic); Valkunas, L., E-mail: leonas.valkunas@ff.vu.lt [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio Avenue 9, build. 3, LT-10222 Vilnius (Lithuania); Center for Physical Sciences and Technology, Institute of Physics, Savanoriu Avenue 231, LT-02300 Vilnius (Lithuania)
2012-08-24
Highlights: Black-Right-Pointing-Pointer Dynamics of excitation within a heterogenous molecular dimer. Black-Right-Pointing-Pointer Excited states can be swapped due to different reorganization energies of monomers. Black-Right-Pointing-Pointer Conventional excitonic basis becomes renormalized due to interaction with the bath. Black-Right-Pointing-Pointer Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.
Excitation Dynamics and Relaxation in a Molecular Heterodimer
Balevicius, V; Abramavicius, D; Mancal, T; Valkunas, L
2011-01-01
The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the energy gap of the molecular excitation, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.
Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics
Wei Zhang
2017-07-01
Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.
Iwaoka, Nobuyuki; Hagita, Katsumi; Takano, Hiroshi
2014-03-01
On the basis of relaxation mode analysis (RMA), we present an efficient method to estimate the linear viscoelasticity of polymer melts in a molecular dynamics (MD) simulation. Slow relaxation phenomena appeared in polymer melts cause a problem that a calculation of the stress relaxation function in MD simulations, especially in the terminal time region, requires large computational efforts. Relaxation mode analysis is a method that systematically extracts slow relaxation modes and rates of the polymer chain from the time correlation of its conformations. We show the computational cost may be drastically reduced by combining a direct calculation of the stress relaxation function based on the Green-Kubo formula with the relaxation rates spectra estimated by RMA. N. I. acknowledges the Graduate School Doctoral Student Aid Program from Keio University.
Calandrini, V. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Synchrotron Soleil, L' Orme de Merisiers, B.P. 48, 91192 Gif-sur-Yvette (France); Hamon, V. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Hinsen, K. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Synchrotron Soleil, L' Orme de Merisiers, B.P. 48, 91192 Gif-sur-Yvette (France); Calligari, P. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Institut Laue-Langevin, 6 Rue Jules Horowitz, B.P. 156, 38042 Grenoble (France); Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France); Bellissent-Funel, M.-C. [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France); Kneller, G.R. [Centre de Biophysique Moleculaire, Rue Charles Sadron, 45071 Orleans (France); Synchrotron Soleil, L' Orme de Merisiers, B.P. 48, 91192 Gif-sur-Yvette (France)], E-mail: kneller@cnrs-orleans.fr
2008-04-18
This paper presents a study of the influence of non-denaturing hydrostatic pressure on the relaxation dynamics of lysozyme in solution, which combines molecular dynamics simulations and quasielastic neutron scattering experiments. We compare results obtained at ambient pressure and at 3 kbar. Experiments have been performed at pD 4.6 and at a protein concentration of 60 mg/ml. For both pressures we checked the monodispersity of the protein solution by small angle neutron scattering. To interpret the simulation results and the experimental data, we adopt the fractional Ornstein-Uhlenbeck process as a model for the internal relaxation dynamics of the protein. On the experimental side, global protein motions are accounted for by the model of free translational diffusion, neglecting the much slower rotational diffusion. We find that the protein dynamics in the observed time window from about 1 to 100 ps is slowed down under pressure, while its fractal characteristics is preserved, and that the amplitudes of the motions are reduced by about 20%. The slowing down of the relaxation is reduced with increasing q-values, where more localized motions are seen.
Molecular dynamics simulations of NMR relaxation and diffusion of bulk hydrocarbons and water
Singer, Philip M.; Asthagiri, Dilip; Chapman, Walter G.; Hirasaki, George J.
2017-04-01
Molecular dynamics (MD) simulations are used to investigate 1H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk n-C5H12 to n-C17H36 hydrocarbons and bulk water. The MD simulations of the 1H NMR relaxation times T1,2 in the fast motion regime where T1 =T2 agree with measured (de-oxygenated) T2 data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion DT coefficients calculated using simulation configurations agree with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations.
Molecular Dynamics Simulation on Charge Transfer Relaxation between Myoglobin and Water
CHENG Wei; ZHANG Feng-Shou; ZHANG Bo-Yang; ZHOU Hong-Yu
2007-01-01
Dynamical processes of myoglobin after photon-excited charge transfer between Fe ion and surrounding water anion ale simulated by a molecular dynamics model.The roles of Coulomb interaction effect and water effect in the relaxation process are discussed.It is found that the relaxations before and after charge transfer are similar.Strong Coulomb interactions and less water mobility decrease Coulomb energy fluctuations.An extra transferred charge of Fe ion has impact on water packing with a distance up to 0.86nm.
Molecular excitation dynamics and relaxation quantum theory and spectroscopy
Valkunas, Leonas; Mancal, Tomas
2013-01-01
Meeting the need for a work that brings together quantum theory and spectroscopy to convey excitation processes to advanced students and specialists wishing to conduct research and understand the entire field rather than just single aspects.Written by an experienced author and recognized authority in the field, this text covers numerous applications and offers examples taken from different disciplines. As a result, spectroscopists, molecular physicists, physical chemists, and biophysicists will all find this a must-have for their research. Also suitable as supplementary reading in graduate
Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart
2015-01-22
Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the
A study of internal energy relaxation in shocks using molecular dynamics based models
Li, Zheng, E-mail: zul107@psu.edu; Parsons, Neal, E-mail: neal.parsons@cd-adapco.com [Department of Aerospace Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Levin, Deborah A., E-mail: deblevin@illinois.edu [Department of Aerospace Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801-2935 (United States)
2015-10-14
Recent potential energy surfaces (PESs) for the N{sub 2} + N and N{sub 2} + N{sub 2} systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N{sub 2} + N{sub 2} system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N{sub 2} dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available.
(14)N NQR, relaxation and molecular dynamics of the explosive TNT.
Smith, John A S; Rowe, Michael D; Althoefer, Kaspar; Peirson, Neil F; Barras, Jamie
2015-10-01
Multiple pulse sequences are widely used for signal enhancement in NQR detection applications. Since the various (14)N NQR relaxation times, signal decay times and frequency of each NQR line have a major influence on detection sequence performance, it is important to characterise these parameters and their temperature variation, as fully as possible. In this paper we discuss such measurements for a number of the ν+ and ν- NQR lines of monoclinic and orthorhombic TNT and relate the temperature variation results to molecular dynamics. The temperature variation of the (14)N spin-lattice relaxation times T1 is interpreted as due to hindered rotation of the NO2 group about the C-NO2 bond with an activation energy of 89 kJ mol(-1) for the ortho and para groups of monoclinic TNT and 70 kJ mol(-1) for the para group of orthorhombic TNT.
Fuson, Michael M.
2017-01-01
Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…
Grain Boundary Relaxation in Bi-Crystals: Mechanical Spectroscopy and Molecular Dynamics Simulations
Maier A.-K.
2015-04-01
Full Text Available Different Au-Ag-Cu samples have been studied by mechanical spectroscopy. Both polycrystals and bi-crystals show a relaxation peak at 800 K, accompanied by an elastic modulus change. Since this peak is absent in single crystals it is related to the presence of grain boundaries. Molecular dynamics simulations reveal two microscopic mechanisms, when a shear stress is applied onto a Σ5 grain boundary: at 700 K, the boundary migrates perpendicularly to the boundary plane under an external stress. At 1000 K, only sliding at the boundary is observed. These two mechanisms acting in different temperature intervals are used to model the mechanic response of a polycrystal under an applied stress. The models yield expressions for the relaxation strength Δ and for the relaxation time τ as a function of the grain size. A comparison with the mechanical spectroscopy measurements of polycrystals and the bi-crystals show that the grain boundary sliding model reproduces correctly the characteristics of the grain boundary peak.
Panczyk, Tomasz; Konczak, Lukasz; Zapotoczny, Szczepan; Szabelski, Pawel; Nowakowska, Maria
2015-01-01
In this work we have analyzed the influence of various factors on the transverse relaxation times T2 of water protons in suspension of magnetic nanoparticles. For that purpose we developed a full molecular dynamics force field which includes the effects of dispersion interactions between magnetic nanoparticles and water molecules, electrostatic interactions between charged nanoparticles and magnetic dipole-dipole and dipole-external field interactions. We also accounted for the magnetization reversal within the nanoparticles body frames due to finite magnetic anisotropy barriers. The force field together with the Langevin dynamics imposed on water molecules and the nanoparticles allowed us to monitor the dephasing of water protons in real time. Thus, we were able to determine the T2 relaxation times including the effects of the adsorption of water on the nanoparticles' surfaces, thermal fluctuations of the orientation of nanoparticles' magnetizations as well as the effects of the core-shell architecture of nanoparticles and their agglomeration into clusters. We found that there exists an optimal cluster size for which T2 is minimized and that the retardation of water molecules motion, due to adsorption on the nanoparticles surfaces, has some effect in the measured T2 times. The typical strengths of the external magnetic fields in MRI are enough to keep the magnetizations fixed along the field direction, however, in the case of low magnetic fields, we observed significant enhancement of T2 due to thermal fluctuations of the orientations of magnetizations. Copyright © 2014 Elsevier Inc. All rights reserved.
J Colmenero; A Arbe; F Alvarez; A Narros; D Richter; M Monkenbush; B Farago
2004-07-01
The combination of molecular dynamics simulations and neutron scattering measurements on three different glass-forming polymers (polyisoprene, poly(vinyl ethylene) and polybutadiene) has allowed to establish the existence of a crossover from Gaussian to non-Gaussian behavior for the incoherent scattering function in the -relaxation regime. The deviation from Gaussian behavior observed can be reproduced assuming the existence of a distribution of discrete jump lengths underlying the sublinear diffusion of the atomic motions during the structural relaxation.
Molecular-dynamics study of amorphous SiO{sub 2} relaxation
Fadhilah, Irfan Muhammad, E-mail: irfanmuhammadf@ymail.com [Department of Physics, Universitas Padjadjaran, Jatinangor, Sumedang 45363 (Indonesia); Rosandi, Yudi, E-mail: rosandi@geophys.unpad.ac.id [Theoretical and Computational Geophysics Laboratory, Department of Physics, Universitas Padjadjaran, Jatinangor, Sumedang 45363 (Indonesia)
2015-09-30
Using Molecular-Dynamics simulation we observed the generation of amorphous SiO{sub 2} target from a randomly distributed Si and O atoms. We applied a sequence of annealing of the target with various temperature and quenching to room temperature. The relaxation time required by the system to form SiO{sub 4} tetrahedral mesh after a relatively long simulation time, is studied. The final amorphous target was analyzed using the radial distribution function method, which can be compared with the available theoretical and experimental data. We found that up to 70% of the target atoms form the tetrahedral SiO{sub 4} molecules. The number of formed tetrahedral increases following the growth function and the rate of SiO{sub 4} formation follows Arrhenius law, depends on the annealing temperature. The local structure of amorphous SiO{sub 2} after this treatment agrees well with those reported in some literatures.
Poulsen, Jens Aage; Rossky, Peter J.
2001-11-01
We present a method based on centroid molecular dynamics (CMD) to calculate nonlinear quantum force correlation functions important in the golden rule approach for studying vibrational energy relaxation (VER) in condensed phases. We consider a model of a diatomic molecule in a two-dimensional neon liquid and also a diatomic coupled to a small Helium cluster. The predictions of the theory for the neon bath are compared and found in close agreement with available theories for VER based on the Egelstaff correction factor and Feynman-Kleinert variational theory. For the Helium cluster, the force spectrum obtained from CMD is found to be in slightly better agreement with the exact result than a method based on a cumulant approach. The results support the use of CMD in condensed phase studies of VER when quantum effects are important.
Tacke, Christian
2015-07-01
Multi spin systems with spin 1/2 nuclei and dipolar coupled quadrupolar nuclei can show so called ''quadrupolar dips''. There are two main reasons for this behavior: polarization transfer and relaxation. They look quite alike and without additional research cannot be differentiated easily in most cases. These two phenomena have quite different physical and theoretical backgrounds. For no or very slow dynamics, polarization transfer will take place, which is energy conserving inside the spin system. This effect can entirely be described using quantum mechanics on the spin system. Detailed knowledge about the crystallography is needed, because this affects the relevant hamiltonians directly. For systems with fast enough dynamics, relaxation takes over, and the energy flows from the spin system to the lattice; thus a more complex theoretical description is needed. This description has to include a dynamic model, usually in the form of a spectral density function. Both models should include detailed modelling of the complete spin system. A software library was developed to be able to model complex spin systems. It allows to simulate polarization transfer or relaxation effects. NMR measurements were performed on the protonic conductor K{sub 3}H(SO{sub 4}){sub 2}. A single crystal shows sharp quadrupolar dips at room temperature. Dynamics could be excluded using relaxation measurements and literature values. Thus, a polarization transfer analysis was used to describe those dips with good agreement. As a second system, imidazolium based molecular crystals were analyzed. The quadrupolar dips were expected to be caused by polarization transfer; this was carefully analyzed and found not to be true. A relaxation based analysis shows good agreement with the measured data in the high temperature area. It leverages a two step spectral density function, which indicates two distinct dynamic processes happening in this system.
A C Ribeiro; P J Sebastiao; C Cruz
2003-08-01
We present in this work a review concerning wide frequency range 1 proton NMR relaxation studies performed in compounds exhibiting columnar mesophases, namely the Colho mesophase in the case of a liquid crystal of discotic molecules and the h mesophase in the case of a liquid crystal of biforked molecules. These NMR relaxation studies were performed combining conventional and fast ﬁeld cycling NMR techniques in a frequency range between 100 Hz and 300 MHz. The possibility of probing such a large frequency range has provided a way to effectively distinguish the inﬂuence, on the 1 relaxation proﬁles, of the different molecular movements observed in this type of mesophases. In addition, we present a comparison between the molecular dynamics in columnar (h) and lamellar (SmC) mesophases exhibited by the same biforked compound.
Molecular structure-property correlations from optical nonlinearity and thermal-relaxation dynamics.
Bhattacharyya, Indrajit; Priyadarshi, Shekhar; Goswami, Debabrata
2009-02-01
We apply ultrafast single beam Z-scan technique to measure saturation absorption coefficients and nonlinear-refraction coefficients of primary alcohols at 1560 nm. The nonlinear effects result from vibronic transitions and cubic nonlinear-refraction. To measure the pure total third-order nonlinear susceptibility, we removed thermal effects with a frequency optimized optical-chopper. Our measurements of thermal-relaxation dynamics of alcohols, from 1560 nm thermal lens pump and 780 nm probe experiments revealed faster and slower thermal-relaxation timescales, respectively, from conduction and convection. The faster timescale accurately predicts thermal-diffusivity, which decreases linearly with alcohol chain-lengths since thermal-relaxation is slower in heavier molecules. The relation between thermal-diffusivity and alcohol chain-length confirms structure-property relationship.
Woźniak-Braszak, Aneta
2017-02-01
Molecular dynamics of the solid 3-(trifluoromethyl) benzoic acid containing proton (1)H and fluorine (19)F nuclei was explored by the solid-state NMR off - resonance technique. Contrary to the previous experiments the proton nuclei system I relaxed in the off - resonance effective field B→e while fluorine nuclei system S was saturated for short time in comparison to the relaxation time T1I. New cross - relaxation solid - state NMR off - resonance experiments were conducted on a homebuilt pulse spectrometer operating at the on-resonance frequency of 30.2MHz, at the off - resonance frequency varied between 30.2 and 30.6MHz for protons and at the frequency of 28.411MHz for fluorines, respectively. Based on the experimental data the dispersions of the proton off - resonance spin - lattice relaxation rate ρρ(I), the fluorine off - resonance spin - lattice relaxation rate ρρ(S) and the cross - relaxation rate σρ in the rotating frame were determined. Copyright © 2016 Elsevier Inc. All rights reserved.
Hou Quan-Wen; Cao Bing-Yang
2012-01-01
The phonon relaxation and heat conduction in one-dimensional Fermi-Pasta-Ulam (FPU) β lattices are studied by using molecular dynamics simulations.The phonon relaxation rate,which dominates the length dependence of the FPU β lattice,is first calculated from the energy autocorrelation function for different modes at various temperatures through equilibrium molecular dynamics simulations.We find that the relaxation rate as a function of wave number k is proportional to k1.688,which leads to a N0.41 divergence of the thermal conductivity in the framework of Green-Kubo relation.This is also in good agreement with the data obtained by non-equilibrium molecular dynamics simulations which estimate the length dependence exponent of the thermal conductivity as 0.415.Our results confirm the N2/5divergence in one-dimensional FPU β lattices.The effects of the heat flux on the thermal conductivity are also studied by imposing different temperature differences on the two ends of the lattices.We find that the thermal conductivity is insensitive to the heat flux under our simulation conditions.It implies that the linear response theory is applicable towards the heat conduction in one-dimensional FPUβ lattices.
Liu, Qing; Shi, Chaowei [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Yu, Lu [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China); Zhang, Longhua [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China)
2015-02-13
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.
P. Arosio; M. Corti; Mariani, M; Orsini, F.; Bogani, L.; A. CANESCHI; Lago, J.; Lascialfari, A.
2015-01-01
The spin dynamics of the molecular magnetic chain [Dy(hfac)(3){NIT(C6H4OPh)}] were investigated by means of the Muon Spin Relaxation (mu+SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac)(3){NIT(C6H4OPh)}] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H - 5, 3500, and 16500 Oe) and by performing mu+SR exp...
Nishikawa, Sadakatsu; Kamimura, Eri
2011-02-03
Ultrasonic absorption coefficients in the frequency range of 0.8-220 MHz have been measured in aqueous solution of amitriptyline (3-(10,11-dihydro-5H-dibenzo[a,d]cycloheptene-5-ylidene)-N,N-dimethyl-1-propanamine) in the concentration range from 0.20 to 0.60 mol dm(-3) at 25 °C. A single relaxational phenomenon has been observed, and the relaxation frequency is independent of the concentration. It has been also observed that the amplitude of the relaxational absorption increases linearly with the analytical concentration. From these ultrasonic relaxation data, it has been concluded that the relaxation is associated with a unimolecular reaction due to a conformational change of the solute molecule, such as a structural change due to a rotational motion of a group in the solute molecule. Molecular orbital semiempirical methods using AM1 (Austin model 1) and PM3 (modified neglect of diatomic overlap parametric method 3) have been applied to obtain the standard enthalpy of formation for amitriptyline molecule at various dihedral angles around one of the bonds in alkylamine side chain. The results have shown the two clear minimum standard enthalpies of formation for amitriptyline. From the difference of the two values, the standard enthalpy change between the two stable conformers has been calculated be 2.9 kJ mol(-1). On a rough assumption that the standard enthalpy change reflects the standard free energy change, the equilibrium constant for the rotational isomers has been estimated to be 0.31. Combining this value with the experimental ultrasonic relaxation frequency, the backward and forward rate constants have been evaluated. The standard enthalpy change of the reaction has been also estimated from the concentration dependence of the maximum absorption per wavelength, and it has been close to that calculated by the semiempirical methods. The ultrasonic absorption measurements have been also carried out in amitriptyline solution in the presence of
Encinar, M; Prolongo, M G; Rubio, R G; Ortega, F; Ahmadi, A; Freire, J J
2011-12-01
The effect of the structure of copolymers (random, alternate or diblock) on their dynamics has been studied by dielectric spectroscopy. Six copolymers of styrene and methyl methacrylate (three diblocks, one alternate and two random) have been studied. The results show that the sub- T (g) transitions of the diblock samples can be described by one asymmetric Havriliak-Negami (HN) function, while two are necessary for the rest of the copolymers (β and γ relaxations). The characteristic times of the sub- T (g) relaxations show an Arrhenius temperature dependence and there is a strong coupling of the α and β relaxations at high temperatures. The deconvolution of the merging relaxations has been made in the framework of the Williams Ansatz set out in terms of Havriliak-Negami distributions. Because the 2D (2)H-NMR results excluded any significant contribution from the rotation of the methoxy group of the methacrylate group around the C-OCH(3) bond, the γ relaxation may be assigned to the rotation of the methyl methacrylate group in a styrene-rich environment. The Molecular Dynamics simulations of a poly(methyl methacrylate) homopolymer and of the alternate copolymer are in qualitative agreement with the experimental results, although they predict smaller values for the activation energy of the sub- T (g) relaxations.
Sichani, Mehrdad M.; Spearot, Douglas E.
2016-07-01
The molecular dynamics simulation method is used to investigate the dependence of crystal orientation and shock wave strength on dislocation density evolution in single crystal Cu. Four different shock directions , , , and are selected to study the role of crystal orientation on dislocation generation immediately behind the shock front and plastic relaxation as the system reaches the hydrostatic state. Dislocation density evolution is analyzed for particle velocities between the Hugoniot elastic limit ( up H E L ) for each orientation up to a maximum of 1.5 km/s. Generally, dislocation density increases with increasing particle velocity for all shock orientations. Plastic relaxation for shock in the , , and directions is primarily due to a reduction in the Shockley partial dislocation density. In addition, plastic anisotropy between these orientations is less apparent at particle velocities above 1.1 km/s. In contrast, plastic relaxation is limited for shock in the orientation. This is partially due to the emergence of sessile stair-rod dislocations with Burgers vectors of 1/3 and 1/6. The nucleation of 1/6 dislocations at lower particle velocities is mainly due to the reaction between Shockley partial dislocations and twin boundaries. On the other hand, for the particle velocities above 1.1 km/s, the nucleation of 1/3 dislocations is predominantly due to reaction between Shockley partial dislocations at stacking fault intersections. Both mechanisms promote greater dislocation densities after relaxation for shock pressures above 34 GPa compared to the other three shock orientations.
Molecular Relaxation in Liquids
Bagchi, Biman
2012-01-01
This book brings together many different relaxation phenomena in liquids under a common umbrella and provides a unified view of apparently diverse phenomena. It aligns recent experimental results obtained with modern techniques with recent theoretical developments. Such close interaction between experiment and theory in this area goes back to the works of Einstein, Smoluchowski, Kramers' and de Gennes. Development of ultrafast laser spectroscopy recently allowed study of various relaxation processes directly in the time domain, with time scales going down to picosecond (ps) and femtosecond (fs
Banerjee, Abhishek; Dey, Arnab; Chandrakumar, Narayanan
2016-11-14
Solution-state Overhauser dynamic nuclear polarization (ODNP) at moderate fields, performed by saturating the electron spin resonance (ESR) of a free radical added to the sample of interest, is well known to lead to significant NMR signal enhancements in the steady state, owing to electron-nuclear cross-relaxation. Here it is shown that under conditions which limit radical access to the molecules of interest, the time course of establishment of ODNP can provide a unique window into internuclear cross-relaxation, and reflects relatively slow molecular motions. This behavior, modeled mathematically by a three-spin version of the Solomon equations (one unpaired electron and two nuclear spins), is demonstrated experimentally on the (19) F/(1) H system in ionic liquids. Bulky radicals in these viscous environments turn out to be just the right setting to exploit these effects. Compared to standard nuclear Overhauser effect (NOE) work, the present experiment offers significant improvement in dynamic range and sensitivity, retains usable chemical shift information, and reports on molecular motions in the sub-megahertz (MHz) to tens of MHz range-motions which are not accessed at high fields. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Markelov, Denis A; Falkovich, Stanislav G; Neelov, Igor M; Ilyash, Maxim Yu; Matveev, Vladimir V; Lähderanta, Erkki; Ingman, Petri; Darinskii, Anatolii A
2015-02-07
NMR relaxation experiments are widely used to investigate the local orientation mobility in dendrimers. In particular, the NMR method allows one to measure the spin-lattice relaxation rate, 1/T1, which is connected with the orientational autocorrelation function (ACF) of NMR active groups. We calculate the temperature (Θ) and frequency (ω) dependences of the spin-lattice NMR relaxation rates for segments and NMR active CH2 groups in poly-L-lysine (PLL) dendrimers in water, on the basis of full-atomic molecular dynamics simulations. It is shown that the position of the maximum of 1/T1(ω) depends on the location of the segments inside the dendrimer. This dependence of the maximum is explained by the restricted flexibility of the dendrimer. Such behavior has been predicted recently by the analytical theory based on the semiflexible viscoelastic model. The simulated temperature dependences of 1/T1 for terminal and inner groups in PLL dendrimers of n = 2 and n = 4 generations dissolved in water are in good agreement with the NMR experimental data, which have been obtained for these systems previously by us. It is shown that in the case of PLL dendrimers, the traditional procedure of the interpretation of NMR experimental data - when smaller values of 1/T1 correspond to higher orientation mobility - is applicable to the whole accessible frequency interval only for the terminal groups. For the inner groups, this procedure is valid only at low frequencies.
Zhao, Yinjian
2017-09-01
Aiming at a high simulation accuracy, a Particle-Particle (PP) Coulombic molecular dynamics model is implemented to study the electron-ion temperature relaxation. In this model, the Coulomb's law is directly applied in a bounded system with two cutoffs at both short and long length scales. By increasing the range between the two cutoffs, it is found that the relaxation rate deviates from the BPS theory and approaches the LS theory and the GMS theory. Also, the effective minimum and maximum impact parameters (bmin* and bmax*) are obtained. For the simulated plasma condition, bmin* is about 6.352 times smaller than the Landau length (bC), and bmax* is about 2 times larger than the Debye length (λD), where bC and λD are used in the LS theory. Surprisingly, the effective relaxation time obtained from the PP model is very close to the LS theory and the GMS theory, even though the effective Coulomb logarithm is two times greater than the one used in the LS theory. Besides, this work shows that the PP model (commonly known as computationally expensive) is becoming practicable via GPU parallel computing techniques.
Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng
2017-07-28
The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm(-1)); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.
Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng
2017-07-01
The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm-1); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.
Golysheva, Elena A.; Shevelev, Georgiy Yu.; Dzuba, Sergei A.
2017-08-01
In glassy substances and biological media, dynamical transitions are observed in neutron scattering that manifests itself as deviations of the translational mean-squared displacement, , of hydrogen atoms from harmonic dynamics. In biological media, the deviation occurs at two temperature intervals, at ˜100-150 K and at ˜170-230 K, and it is attributed to the motion of methyl groups in the former case and to the transition from harmonic to anharmonic or diffusive motions in the latter case. In this work, electron spin echo (ESE) spectroscopy—a pulsed version of electron paramagnetic resonance—is applied to study the spin relaxation of nitroxide spin probes and labels introduced in molecular glass former o-terphenyl and in protein lysozyme. The anisotropic contribution to the rate of the two-pulse ESE decay, ΔW, is induced by spin relaxation appearing because of restricted orientational stochastic molecular motion; it is proportional to τc, where is the mean-squared angle of reorientation of the nitroxide molecule around the equilibrium position and τc is the correlation time of reorientation. The ESE time window allows us to study motions with τc τc temperature dependence shows a transition near 240 K, which is in agreement with the literature data on . For spin probes of essentially different size, the obtained data were found to be close, which evidences that motion is cooperative, involving a nanocluster of several neighboring molecules. For the dry lysozyme, the τc values below 260 K were found to linearly depend on the temperature in the same way as it was observed in neutron scattering for . As spin relaxation is influenced only by stochastic motion, the harmonic motions seen in ESE must be overdamped. In the hydrated lysozyme, ESE data show transitions near 130 K for all nitroxides, near 160 K for the probe located in the hydration layer, and near 180 K for the label in the protein interior. For this system, the two latter transitions are not
Baranowski, M.; Woźniak-Braszak, A.; Jurga, K.
2016-01-01
The paper presents the benefits of using fast adiabatic passage for the study of molecular dynamics in the solid state heteronuclear systems in the laboratory frame. A homemade pulse spectrometer operating at the frequency of 30.2 MHz and 28.411 MHz for protons and fluorines, respectively, has been enhanced with microcontroller direct digital synthesizer DDS controller [1-4]. This work briefly describes how to construct a low-cost and easy-to-assemble adiabatic extension set for homemade and commercial spectrometers based on recently very popular Arduino shields. The described set was designed for fast adiabatic generation. Timing and synchronization problems are discussed. The cross-relaxation experiments with different initial states of the two spin systems have been performed. Contrary to our previous work [5] where the steady-state NOE experiments were conducted now proton spins 1H are polarized in the magnetic field B0 while fluorine spins 19F are perturbed by selective saturation for a short time and then the system is allowed to evolve for a period in the absence of a saturating field. The adiabatic passage application leads to a reversal of magnetization of fluorine spins and increases the amplitude of the signal.
Dynamical theory of spin relaxation
Field, Timothy R.; Bain, Alex D.
2013-02-01
The dynamics of a spin system is usually calculated using the density matrix. However, the usual formulation in terms of the density matrix predicts that the signal will decay to zero, and does not address the issue of individual spin dynamics. Using stochastic calculus, we develop a dynamical theory of spin relaxation, the origins of which lie in the component spin fluctuations. This entails consideration of random pure states for individual protons, and how these pure states are correctly combined when the density matrix is formulated. Both the lattice and the spins are treated quantum mechanically. Such treatment incorporates both the processes of spin-spin and (finite temperature) spin-lattice relaxation. Our results reveal the intimate connections between spin noise and conventional spin relaxation.
Glowacki, David R; Rodgers, W J; Shannon, Robin; Robertson, Struan H; Harvey, Jeremy N
2017-04-28
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of
Fingerprinting Molecular Relaxation in Deformed Polymers
Wang, Zhe; Lam, Christopher N.; Chen, Wei-Ren; Wang, Weiyu; Liu, Jianning; Liu, Yun; Porcar, Lionel; Stanley, Christopher B.; Zhao, Zhichen; Hong, Kunlun; Wang, Yangyang
2017-07-01
The flow and deformation of macromolecules is ubiquitous in nature and industry, and an understanding of this phenomenon at both macroscopic and microscopic length scales is of fundamental and practical importance. Here, we present the formulation of a general mathematical framework, which could be used to extract, from scattering experiments, the molecular relaxation of deformed polymers. By combining and modestly extending several key conceptual ingredients in the literature, we show how the anisotropic single-chain structure factor can be decomposed by spherical harmonics and experimentally reconstructed from its cross sections on the scattering planes. The resulting wave-number-dependent expansion coefficients constitute a characteristic fingerprint of the macromolecular deformation, permitting detailed examinations of polymer dynamics at the microscopic level. We apply this approach to survey a long-standing problem in polymer physics regarding the molecular relaxation in entangled polymers after a large step deformation. The classical tube theory of Doi and Edwards predicts a fast chain retraction process immediately after the deformation, followed by a slow orientation relaxation through the reptation mechanism. This chain retraction hypothesis, which is the keystone of the tube theory for macromolecular flow and deformation, is critically examined by analyzing the fine features of the two-dimensional anisotropic spectra from small-angle neutron scattering by entangled polystyrenes. We show that the unique scattering patterns associated with the chain retraction mechanism are not experimentally observed. This result calls for a fundamental revision of the current theoretical picture for nonlinear rheological behavior of entangled polymeric liquids.
Lidorikis, Elefterios; Bachlechner, Martina E.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
2005-09-01
A hybrid atomistic-continuum simulation approach has been implemented to study strain relaxation in lattice-mismatched Si/Si3N4 nanopixels on a Si(111) substrate. We couple the molecular-dynamics (MD) and finite-element simulation approaches to provide an atomistic description near the interface and a continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are validated against full multimillion-atom MD simulations. We find that strain relaxation in Si/Si3N4 nanopixels may occur through the formation of a network of interfacial domain boundaries reminiscent of interfacial misfit dislocations. They result from the nucleation of domains of different interfacial bonding at the free edges and corners of the nanopixel, and subsequent to their creation they propagate inwards. We follow the motion of the domain boundaries and estimate a propagation speed of about ˜2.5×103m/s . The effects of temperature, nanopixel architecture, and film structure on strain relaxation are also investigated. We find: (i) elevated temperature increases the interfacial domain nucleation rates; (ii) a thin compliant Si layer between the film and the substrate plays a beneficial role in partially suppressing strain relaxation; and (iii) additional control over the interface morphology may be achieved by varying the film structure.
Arosio, Paolo, E-mail: paolo.arosio@guest.unimi.it; Orsini, Francesco [Department of Physics, Università degli Studi di Milano, and INSTM, Milano (Italy); Corti, Maurizio [Department of Physics, Università degli Studi di Pavia and INSTM, Pavia (Italy); Mariani, Manuel [Department of Physics and Astronomy, Università degli Studi di Bologna, Bologna (Italy); Bogani, Lapo [Physikalisches Institut, Universität Stuttgart, Stuttgart (Germany); Caneschi, Andrea [INSTM and Department of Chemistry, University of Florence, Firenze (Italy); Lago, Jorge [Departamento de Quimica Inorganica, Universidad del Pais Vasco, Bilbao (Spain); Lascialfari, Alessandro [Department of Physics, Università degli Studi di Milano, and INSTM, Milano (Italy); Centro S3, Istituto Nanoscienze - CNR, Modena (Italy)
2015-05-07
The spin dynamics of the molecular magnetic chain [Dy(hfac){sub 3}(NIT(C{sub 6}H{sub 4}OPh))] were investigated by means of the Muon Spin Relaxation (μ{sup +}SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac){sub 3}(NIT(C{sub 6}H{sub 4}OPh))] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ{sup +}SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λ{sub interm}(T), associated with the intermediate relaxing component. The experimental λ{sub interm}(T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ{sub 0} exp(Δ/k{sub B}T), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state.
Das, Anuradha; Das, Suman; Biswas, Ranjit, E-mail: ranjit@bose.res.in [Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, West Bengal 700098 (India)
2015-01-21
Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.
Ladd, A.J.C.
1988-08-01
The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.
Bergstra, J.A.; Bethke, I.
2002-01-01
Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model
Reale, Riccardo; English, Niall J; Garate, José-Antonio; Marracino, Paolo; Liberti, Micaela; Apollonio, Francesca
2013-11-28
Water self-diffusion and the dipolar response of the selectivity filter within human aquaporin 4 have been studied using molecular dynamics (MD) simulations in the absence and presence of pulses of external static and alternating electric fields. The pulses were approximately 50 and 100 ns in duration and 0.0065 V/Å in (r.m.s.) intensity and were either static or else 2.45 or 100 GHz in frequency and applied both along and perpendicular to the channels. In addition, the relaxation of the aquaporin, water self-diffusion and gating dynamics following cessation of the impulses was studied. In previous work it was determined that switches in the dihedral angle of the selectivity filter led to boosting of water permeation events within the channels, in the presence of identical external static and alternating electric fields, although applied continuously. Here the application of field impulses (and subsequently, upon removal) has shown that it is the dipolar orientation of the histidine-201 residue in the selectivity filter which governs the dihedral angle, and hence influences water self-diffusion; this constitutes an appropriate order parameter. The dipolar response of this residue to the applied field leads to the adoption of four distinct states, which we modelled as time-homogeneous Markov jump processes, and may be distinguished in the potential of mean force (PMF) as a function of the dipolar orientation of histidine-201. The observations of enhanced "dipolar flipping" of H201 serve to explain increased levels of water self-diffusion within aquaporin channels during, and immediately following, field impulses, although the level of statistical certainty here is lower. Given the appreciable size of the energy barriers evident in PMFs computed directly from deterministic MD (whether in the absence or presence of external fields), metadynamics calculations were undertaken to explore the free-energy landscape of histidine-201 orientation with greater accuracy and
Relaxation time in disordered molecular systems
Rocha, Rodrigo P. [Departamento de Física, Universidade Federal de Santa Catarina, 88040-900 Florianópolis-SC (Brazil); Freire, José A., E-mail: jfreire@fisica.ufpr.br [Departamento de Física, Universidade Federal do Paraná, 81531-990 Curitiba-PR (Brazil)
2015-05-28
Relaxation time is the typical time it takes for a closed physical system to attain thermal equilibrium. The equilibrium is brought about by the action of a thermal reservoir inducing changes in the system micro-states. The relaxation time is intuitively expected to increase with system disorder. We derive a simple analytical expression for this dependence in the context of electronic equilibration in an amorphous molecular system model. We find that the disorder dramatically enhances the relaxation time but does not affect its independence of the nature of the initial state.
Protein dynamics: from rattling in a cage to structural relaxation
Khodadadia, S.; Sokolov, A.P.
2015-01-01
We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss th
Relaxation Dynamics in Heme Proteins.
Scholl, Reinhard Wilhelm
A protein molecule possesses many conformational substates that are likely arranged in a hierarchy consisting of a number of tiers. A hierarchical organization of conformational substates is expected to give rise to a multitude of nonequilibrium relaxation phenomena. If the temperature is lowered, transitions between substates of higher tiers are frozen out, and relaxation processes characteristic of lower tiers will dominate the observational time scale. This thesis addresses the following questions: (i) What is the energy landscape of a protein? How does the landscape depend on the environment such as pH and viscosity, and how can it be connected to specific structural parts? (ii) What relaxation phenomena can be observed in a protein? Which are protein specific, and which occur in other proteins? How does the environment influence relaxations? (iii) What functional form best describes relaxation functions? (iv) Can we connect the motions to specific structural parts of the protein molecule, and are these motions important for the function of the protein?. To this purpose, relaxation processes after a pressure change are studied in carbonmonoxy (CO) heme proteins (myoglobin-CO, substrate-bound and substrate-free cytochrome P450cam-CO, chloroperoxidase-CO, horseradish peroxidase -CO) between 150 K and 250 K using FTIR spectroscopy to monitor the CO bound to the heme iron. Two types of p -relaxation experiments are performed: p-release (200 to ~eq40 MPa) and p-jump (~eq40 to 200 MPa) experiments. Most of the relaxations fall into one of three groups and are characterized by (i) nonexponential time dependence and non-Arrhenius temperature dependence (FIM1( nu), FIM1(Gamma)); (ii) exponential time dependence and non-Arrhenius temperature dependence (FIM0(A_{i}to A_{j})); exponential time dependence and Arrhenius temperature dependence (FIMX( nu)). The influence of pH is studied in myoglobin-CO and shown to have a strong influence on the substate population of the
Iuchi, Satoru; Koga, Nobuaki [Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan)
2015-12-31
A model electronic Hamiltonian of [Fe(bpy){sub 3}]{sup 2+}, which was recently refined for use in molecular dynamics simulations, is reviewed with some additional results. In particular, the quality of the refined model Hamiltonian is examined in terms of the vibrational frequencies and solvation structures of the lowest singlet and quintet states.
Protein dynamics from nuclear magnetic relaxation.
Charlier, Cyril; Cousin, Samuel F; Ferrage, Fabien
2016-05-01
Nuclear magnetic resonance is a ubiquitous spectroscopic tool to explore molecules with atomic resolution. Nuclear magnetic relaxation is intimately connected to molecular motions. Many methods and models have been developed to measure and interpret the characteristic rates of nuclear magnetic relaxation in proteins. These approaches shed light on a rich and diverse range of motions covering timescales from picoseconds to seconds. Here, we introduce some of the basic concepts upon which these approaches are built and provide a series of illustrations.
On the Relaxation Dynamics of Disordered Systems
Dobramysl, Ulrich
We investigate the properties of two distinct disordered systems: the two-species predator-prey Lotka-Volterra model with rate variability, and an elastic line model to simulate vortex lines in type-II superconductors. We study the effects of intrinsic demographic variability with inheritance in the reaction rates of the Lotka-Volterra model via zero-dimensional Monte Carlo simulations as well as two-dimensional lattice simulations. Individuals of each species are assigned inheritable predation efficiencies during their creation, leading to evolutionary dynamics and thus population-level optimization. We derive an effective subspecies mean-field theory and compare its results to our numerical data. Furthermore, we introduce environmental variability via quenched spatial reaction-rate randomness. We investigate the competing effects and relative importance of the two types of variability, and find that both lead to a remarkable enhancement of the species densities, while the aforementioned optimization effects are essentially neutral in the densities. Additionally, we collected extinction time histograms for small systems and find a marked increase in the stability of the populations against extinction due to the presence of variability. We employ an elastic line model to investigate the steady-state properties and non-equilibrium relaxation kinetics of magnetic vortex lines in disordered type-II superconductors. To this end, we developed a versatile and efficient Langevin molecular dynamics simulation code, allowing us to do a careful study of samples with or without vortex-vortex interactions or disorder allows us to disentangle the various complex relaxational features present in this system and investigate their origin. In particular, we compare disordered samples with randomly distributed point defects versus correlated columnar defects. We extract two-time quantities such as the mean-square displacement, the height and density correlations, to investigate the
Zhu, Ming; Liu, Tingting; Wang, Shu; Zhang, Kesheng
2017-08-01
Existing two-frequency reconstructive methods can only capture primary (single) molecular relaxation processes in excitable gases. In this paper, we present a reconstructive method based on the novel decomposition of frequency-dependent acoustic relaxation spectra to capture the entire molecular multimode relaxation process. This decomposition of acoustic relaxation spectra is developed from the frequency-dependent effective specific heat, indicating that a multi-relaxation process is the sum of the interior single-relaxation processes. Based on this decomposition, we can reconstruct the entire multi-relaxation process by capturing the relaxation times and relaxation strengths of N interior single-relaxation processes, using the measurements of acoustic absorption and sound speed at 2N frequencies. Experimental data for the gas mixtures CO2-N2 and CO2-O2 validate our decomposition and reconstruction approach.
De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe
2014-12-09
A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.
Plasma Relaxation Dynamics Moderated by Current Sheets
Dewar, Robert; Bhattacharjee, Amitava; Yoshida, Zensho
2014-10-01
Ideal magnetohydrodynamics (IMHD) is strongly constrained by an infinite number of microscopic constraints expressing mass, entropy and magnetic flux conservation in each infinitesimal fluid element, the latter preventing magnetic reconnection. By contrast, in the Taylor-relaxed equilibrium model all these constraints are relaxed save for global magnetic flux and helicity. A Lagrangian is presented that leads to a new variational formulation of magnetized fluid dynamics, relaxed MHD (RxMHD), all static solutions of which are Taylor equilibrium states. By postulating that some long-lived macroscopic current sheets can act as barriers to relaxation, separating the plasma into multiple relaxation regions, a further generalization, multi-relaxed MHD (MRxMHD), is developed. These concepts are illustrated using a simple two-region slab model similar to that proposed by Hahm and Kulsrud--the formation of an initial shielding current sheet after perturbation by boundary rippling is calculated using MRxMHD and the final island state, after the current sheet has relaxed through a reconnection sequence, is calculated using RxMHD. Australian Research Council Grant DP110102881.
Relaxation Dynamics of Semiflexible Fractal Macromolecules
Jonas Mielke
2016-07-01
Full Text Available We study the dynamics of semiflexible hyperbranched macromolecules having only dendritic units and no linear spacers, while the structure of these macromolecules is modeled through T-fractals. We construct a full set of eigenmodes of the dynamical matrix, which couples the set of Langevin equations. Based on the ensuing relaxation spectra, we analyze the mechanical relaxation moduli. The fractal character of the macromolecules reveals itself in the storage and loss moduli in the intermediate region of frequencies through scaling, whereas at higher frequencies, we observe the locally-dendritic structure that is more pronounced for higher stiffness.
Solar, M.; Binder, K.; Paul, W.
2017-05-01
Molecular dynamics simulations of a chemically realistic model for 1,4-polybutadiene in a thin film geometry confined by two graphite walls are presented. Previous work on melts in the bulk has shown that the model faithfully reproduces static and dynamic properties of the real material over a wide temperature range. The present work studies how these properties change due to nano-confinement. The focus is on orientational correlations observable in nuclear magnetic resonance experiments and on the local intermediate incoherent neutron scattering function, Fs(qz, z, t), for distances z from the graphite walls in the range of a few nanometers. Temperatures from about 2Tg down to about 1.15Tg, where Tg is the glass transition temperature in the bulk, are studied. It is shown that weakly attractive forces between the wall atoms and the monomers suffice to effectively bind a polymer coil that is near the wall. For a wide regime of temperatures, the Arrhenius-like adsorption/desorption kinetics of the monomers is the slowest process, while very close to Tg the Vogel-Fulcher-Tammann-like α-relaxation takes over. The α-process is modified only for z ≤1.2 nm due to the density changes near the walls, less than expected from studies of coarse-grained (bead-spring-type) models. The weakness of the surface effects on the glass transition in this case is attributed to the interplay of density changes near the wall with the torsional potential. A brief discussion of pertinent experiments is given.
Generalized extended Navier-Stokes theory: Multiscale spin relaxation in molecular fluids
Hansen, Jesper Schmidt
2013-01-01
This paper studies the relaxation of the molecular spin angular velocity in the framework of generalized extended Navier-Stokes theory. Using molecular dynamics simulations, it is shown that for uncharged diatomic molecules the relaxation time decreases with increasing molecular moment of inertia...... per unit mass. In the regime of large moment of inertia the fast relaxation is wave-vector independent and dominated by the coupling between spin and the fluid streaming velocity, whereas for small inertia the relaxation is slow and spin diffusion plays a significant role. The fast wave...
Relaxation Dynamics of Nanoparticle-Tethered Polymer Chains
Kim, Sung A
2015-09-08
© 2015 American Chemical Society. Relaxation dynamics of nanoparticle-tethered cis-1,4-polyisoprene (PI) are investigated using dielectric spectroscopy and rheometry. A model system composed of polymer chains densely grafted to spherical SiO
Nima Kasraie
2011-01-01
Full Text Available The aims of this study were to determine whether standard extracellular contrast agents of Gd(III ions in combination with a polymeric entity susceptible to hydrolytic degradation over a finite period of time, such as Hyaluronic Acid (HA, have sufficient vascular residence time to obtain comparable vascular imaging to current conventional compounds and to obtain sufficient data to show proof of concept that HA with Gd-DTPA ligands could be useful as vascular imaging agents. We assessed the dynamic relaxivity of the HA bound DTPA compounds using a custom-made phantom, as well as relaxation rates at 10.72 MHz with concentrations ranging between 0.09 and 7.96 mM in phosphate-buffered saline. Linear dependences of static longitudinal relaxation rate (R1 on concentration were found for most measured samples, and the HA samples continued to produce high signal strength after 24 hours after injection into a dialysis cassette at 3T, showing superior dynamic relaxivity values compared to conventional contrast media such as Gd-DTPA-BMA.
Dynamic isotope effects on relaxation of quadrupolar nuclei in 12 simple organic molecules
毛希安; andM.Holz
1995-01-01
Dynamic isotope effects on relaxation rate of quadrupolar nuclei are preliminarily reported. The relaxation rates of 17O and 14N in 12 simple organic molecules and their 18 corresponding deuterated species have been systematically measured. The principal components of the molecular inertia tensors have been calculated. The results show that there is an intrinsic correlation between the dynamic isotope effects of the relaxation rate and the static isotope effects of the molecular inertia. The concepts of molecular collision frequency and translation-rotation coupling have been introduced into the NMR relaxation theory. Therefore, a reasonable explanation of the experimental results has been given.
TURBULENCE DECAY AND CLOUD CORE RELAXATION IN MOLECULAR CLOUDS
Gao, Yang; Law, Chung K. [Center for Combustion Energy, Tsinghua University, Beijing 100084 (China); Xu, Haitao, E-mail: gaoyang-00@mails.tsinghua.edu.cn [Max Planck Institute for Dynamics and Self-Organization (MPIDS), D-37077 Göttingen (Germany)
2015-02-01
The turbulent motion within molecular clouds is a key factor controlling star formation. Turbulence supports molecular cloud cores from evolving to gravitational collapse and hence sets a lower bound on the size of molecular cloud cores in which star formation can occur. On the other hand, without a continuous external energy source maintaining the turbulence, such as in molecular clouds, the turbulence decays with an energy dissipation time comparable to the dynamic timescale of clouds, which could change the size limits obtained from Jean's criterion by assuming constant turbulence intensities. Here we adopt scaling relations of physical variables in decaying turbulence to analyze its specific effects on the formation of stars. We find that the decay of turbulence provides an additional approach for Jeans' criterion to be achieved, after which gravitational infall governs the motion of the cloud core. This epoch of turbulence decay is defined as cloud core relaxation. The existence of cloud core relaxation provides a more complete understanding of the effect of the competition between turbulence and gravity on the dynamics of molecular cloud cores and star formation.
Relaxation dynamics of multilayer triangular Husimi cacti
Galiceanu, Mircea; Jurjiu, Aurel
2016-09-01
We focus on the relaxation dynamics of multilayer polymer structures having, as underlying topology, the Husimi cactus. The relaxation dynamics of the multilayer structures is investigated in the framework of generalized Gaussian structures model using both Rouse and Zimm approaches. In the Rouse type-approach, we determine analytically the complete eigenvalues spectrum and based on it we calculate the mechanical relaxation moduli (storage and loss modulus) and the average monomer displacement. First, we monitor these physical quantities for structures with a fixed generation number and we increase the number of layers, such that the linear topology will smoothly come into play. Second, we keep constant the size of the structures, varying simultaneously two parameters: the generation number of the main layer, G, and the number of layers, c. This fact allows us to study in detail the crossover from a pure Husimi cactus behavior to a predominately linear chain behavior. The most interesting situation is found when the two limiting topologies cancel each other. For this case, we encounter in the intermediate frequency/time domain regions of constant slope for different values of the parameter set (G, c) and we show that the number of layers follows an exponential-law of G. In the Zimm-type approach, which includes the hydrodynamic interactions, the quantities that describe the mechanical relaxation dynamics do not show scaling behavior as in the Rouse model, except the limiting case, namely, a very high number of layers and low generation number.
Schlüter, Steffen [School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis Oregon USA; Department Soil Physics, Helmholtz-Centre for Environmental Research-UFZ, Halle Germany; Berg, Steffen [Shell Global Solutions International B.V., Rijswijk Netherlands; Li, Tianyi [School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis Oregon USA; Vogel, Hans-Jörg [Department Soil Physics, Helmholtz-Centre for Environmental Research-UFZ, Halle Germany; Institut für Agrar- und Ernährungswissenschaften, Martin-Luther-Universität Halle-Wittenberg, Halle Germany; Wildenschild, Dorthe [School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis Oregon USA
2017-06-01
The relaxation dynamics toward a hydrostatic equilibrium after a change in phase saturation in porous media is governed by fluid reconfiguration at the pore scale. Little is known whether a hydrostatic equilibrium in which all interfaces come to rest is ever reached and which microscopic processes govern the time scales of relaxation. Here we apply fast synchrotron-based X-ray tomography (X-ray CT) to measure the slow relaxation dynamics of fluid interfaces in a glass bead pack after fast drainage of the sample. The relaxation of interfaces triggers internal redistribution of fluids, reduces the surface energy stored in the fluid interfaces, and relaxes the contact angle toward the equilibrium value while the fluid topology remains unchanged. The equilibration of capillary pressures occurs in two stages: (i) a quick relaxation within seconds in which most of the pressure drop that built up during drainage is dissipated, a process that is to fast to be captured with fast X-ray CT, and (ii) a slow relaxation with characteristic time scales of 1–4 h which manifests itself as a spontaneous imbibition process that is well described by the Washburn equation for capillary rise in porous media. The slow relaxation implies that a hydrostatic equilibrium is hardly ever attained in practice when conducting two-phase experiments in which a flux boundary condition is changed from flow to no-flow. Implications for experiments with pressure boundary conditions are discussed.
Using relaxational dynamics to reduce network congestion
Piontti, Ana L. Pastore y.; La Rocca, Cristian E.; Toroczkai, Zoltán; Braunstein, Lidia A.; Macri, Pablo A.; López, Eduardo
2008-09-01
We study the effects of relaxational dynamics on congestion pressure in scale-free (SF) networks by analyzing the properties of the corresponding gradient networks (Toroczkai and Bassler 2004 Nature 428 716). Using the Family model (Family and Bassler 1986 J. Phys. A: Math. Gen. 19 L441) from surface-growth physics as single-step load-balancing dynamics, we show that the congestion pressure considerably drops on SF networks when compared with the same dynamics on random graphs. This is due to a structural transition of the corresponding gradient network clusters, which self-organize so as to reduce the congestion pressure. This reduction is enhanced when lowering the value of the connectivity exponent λ towards 2.
Measuring Propellant Stress Relaxation Modulus Using Dynamic Mechanical Analyzer
2017-03-29
P. N., Singh, P. P., and Bhattacharya, B., “Determination of Activation Energy of Relaxation Events in Composite Solid Propellants by Dynamic...Article 3. DATES COVERED (From - To) 04 August 2016 – 29 March 2017 4. TITLE AND SUBTITLE Measuring Propellant Stress Relaxation Modulus Using Dynamic...ERC 14. ABSTRACT A method for determining the stress relaxation master curve of solid rocket propellants was developed. The propellant was tested in
Vibrational relaxation of guest and host in mixed molecular crystals
Hill, Jeffrey R.; Chronister, Eric L.; Chang, Ta-Chau; Kim, Hackjin; Postlewaite, Jay C.; Dlott, Dana D.
1988-02-01
Vibrational relaxation (VR) of dilute impurity molecules (naphthalene, anthracene) in crystalline host matrices (durene, naphthalene) is studied with the ps photon echo technique. The results obtained by echoes on vibrations in the electronically excited state are compared to previous ps time delayed coherent Raman studies of ground state vibrations of the pure host matrix. The relaxation channels for guest and host, and the effects of molecular and crystal structure on VR rates are determined.
Surface hopping investigation of the relaxation dynamics in radical cations
Assmann, Mariana; Matsika, Spiridoula, E-mail: smatsika@temple.edu [Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122 (United States); Weinacht, Thomas [Department of Physics, Stony Brook University, Stony Brook, New York 11794 (United States)
2016-01-21
Ionization processes can lead to the formation of radical cations with population in several ionic states. In this study, we examine the dynamics of three radical cations starting from an excited ionic state using trajectory surface hopping dynamics in combination with multiconfigurational electronic structure methods. The efficiency of relaxation to the ground state is examined in an effort to understand better whether fragmentation of cations is likely to occur directly on excited states or after relaxation to the ground state. The results on cyclohexadiene, hexatriene, and uracil indicate that relaxation to the ground ionic state is very fast in these systems, while fragmentation before relaxation is rare. Ultrafast relaxation is facilitated by the close proximity of electronic states and the presence of two- and three-state conical intersections. Examining the properties of the systems in the Franck-Condon region can give some insight into the subsequent dynamics.
Relaxation towards phase-locked dynamics in long Josephson junctions
Salerno, M.; Grønbech-Jensen, Niels; Samuelsen, Mogens Rugholm
1995-01-01
We study the relaxation phenomenon towards phase-locked dynamics in long Josephson junctions. In particular the dependence of the relaxation frequency for the equal time of flight solution on the junction parameters is derived. The analysis is based on a phase-locked map and is compared with dire...
Siwko, Magdalena E; Corni, Stefano
2013-04-28
Proteins immobilized on inorganic surfaces are important in technological fields such as biosensors, enzymatic biofuel cells and biomolecular electronics. In these frameworks, it has been demonstrated that some proteins are able to keep their functionality, although the latter may be somewhat modified by the interaction with the surface. Cytochrome C, an heme-based electron transfer protein, has been found to be able to exchange electrons with the gold surface on which it is immobilized, but some deviations from the expected electron transfer rates were evidenced [C. A. Bortolotti, et al., J. Phys. Chem. C 2007, 111, 12100-12105]. In this work we have used molecular dynamics simulations of (native and mutated) yeast cytochrome C supported on Au(111) to investigate the microscopic picture behind the experimental behavior of the molecule. In particular, we have focused on the structural re-arrangements due to the interactions with the surface. We found that, despite being secondary-structure preserving, they can profoundly affect protein-surface electronic coupling and, in turn, electron transfer rates, explaining experimental findings. The conformational flexibility of the protein in the region of the protein-surface bond is thus pivotal in determining the resulting ET functionality of the immobilized protein.
Ultrafast NMR T1 relaxation measurements: probing molecular properties in real time.
Smith, Pieter E S; Donovan, Kevin J; Szekely, Or; Baias, Maria; Frydman, Lucio
2013-09-16
The longitudinal relaxation properties of NMR active nuclei carry useful information about the site-specific chemical environments and about the mobility of molecular fragments. Molecular mobility is in turn a key parameter reporting both on stable properties, such as size, as well as on dynamic ones, such as transient interactions and irreversible aggregation. In order to fully investigate the latter, a fast sampling of the relaxation parameters of transiently formed molecular species may be needed. Nevertheless, the acquisition of longitudinal relaxation data is typically slow, being limited by the requirement that the time for which the nucleus relaxes be varied incrementally until a complete build-up curve is generated. Recently, a number of single-shot-inversion-recovery methods have been developed capable of alleviating this need; still, these may be challenged by either spectral resolution restrictions or when coping with very fast relaxing nuclei. Here, we present a new experiment to measure the T1s of multiple nuclear spins that experience fast longitudinal relaxation, while retaining full high-resolution chemical shift information. Good agreement is observed between T1s measured with conventional means and T1s measured using the new technique. The method is applied to the real-time investigation of the reaction between D-xylose and sodium borate, which is in turn elucidated with the aid of ancillary ultrafast and conventional 2D TOCSY measurements. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Dynamical Non-Equilibrium Molecular Dynamics
Giovanni Ciccotti
2013-12-01
Full Text Available In this review, we discuss the Dynamical approach to Non-Equilibrium Molecular Dynamics (D-NEMD, which extends stationary NEMD to time-dependent situations, be they responses or relaxations. Based on the original Onsager regression hypothesis, implemented in the nineteen-seventies by Ciccotti, Jacucci and MacDonald, the approach permits one to separate the problem of dynamical evolution from the problem of sampling the initial condition. D-NEMD provides the theoretical framework to compute time-dependent macroscopic dynamical behaviors by averaging on a large sample of non-equilibrium trajectories starting from an ensemble of initial conditions generated from a suitable (equilibrium or non-equilibrium distribution at time zero. We also discuss how to generate a large class of initial distributions. The same approach applies also to the calculation of the rate constants of activated processes. The range of problems treatable by this method is illustrated by discussing applications to a few key hydrodynamic processes (the “classical” flow under shear, the formation of convective cells and the relaxation of an interface between two immiscible liquids.
Relaxation Dynamics in Condensation on Weighted Scale-Free Networks
MENG Xin-He; TANG Ming; WANG Peng; LIU Zong-Hua
2008-01-01
Most of the realistic networks are weighted scale-free networks. How this structure influences the conden-sation on it is a challenging problem. Recently, we make a first step to discuss its condensation [Phys. Rev. E 74 (2006) 036101] and here we focus on its evolutionary process of phase transition. In order to show how the weighted transport influences the dynamical properties, we study the relaxation dynamics in a zero range process on weighted scale-free networks. We find that there is a hierarchical relaxation dynamics in the evolution and there is a scaling relation between the relaxation time and the jumping exponent. The relaxation dynamics can be illustrated by a mean-field equation. The theoretical predictions are confirmed by our numerical simulations.
Thermal relaxation of molecular oxygen in collisions with nitrogen atoms
Andrienko, Daniil A.; Boyd, Iain D.
2016-07-01
Investigation of O2-N collisions is performed by means of the quasi-classical trajectory method on the two lowest ab initio potential energy surfaces at temperatures relevant to hypersonic flows. A complete set of bound-bound and bound-free transition rates is obtained for each precollisional rovibrational state. Special attention is paid to the vibrational and rotational relaxations of oxygen as a result of chemically non-reactive interaction with nitrogen atoms. The vibrational relaxation of oxygen partially occurs via the formation of an intermediate NO2 complex. The efficient energy randomization results in rapid vibrational relaxation at low temperatures, compared to other molecular systems with a purely repulsive potential. The vibrational relaxation time, computed by means of master equation studies, is nearly an order of magnitude lower than the relaxation time in N2-O collisions. The rotational nonequilibrium starts to play a significant effect at translational temperatures above 8000 K. The present work provides convenient relations for the vibrational and rotational relaxation times as well as for the quasi-steady dissociation rate coefficient and thus fills a gap in data due to a lack of experimental measurements for this system.
Dynamics of cosmological relaxation after reheating
Choi, Kiwoon; Sekiguchi, Toyokazu
2016-01-01
We examine if the cosmological relaxation mechanism, which was proposed recently as a new solution to the hierarchy problem, can be compatible with high reheating temperature well above the weak scale. As the barrier potential disappears at high temperature, the relaxion rolls down further after the reheating, which may ruin the successful implementation of the relaxation mechanism. It is noted that if the relaxion is coupled to a dark gauge boson, the new frictional force arising from dark gauge boson production can efficiently slow down the relaxion motion, which allows the relaxion to be stabilized after the electroweak phase transition for a wide range of model parameters, while satisfying the known observational constraints.
Yang, Hongqin; Tang, Peixiao; Tang, Bin; Huang, Yanmei; He, Jiawei; Li, Shanshan; Li, Hui
2017-06-01
The interactions between lafutidine (LAF) and calf thymus DNA (ctDNA) have been investigated both experimentally and theoretically. UV-vis absorption studies confirmed that LAF binds to ctDNA through non-covalent interactions. Fluorescence quenching and time-resolved fluorescence spectroscopy studies showed that the binding of LAF with ctDNA occurred through static quenching mechanism, resulting in the formation of a LAF-ctDNA complex. The binding constants (K) of the complex were found to be around 10(3)M(-1) via NMR relaxation rates and fluorescence data, and the calculated thermodynamic parameters indicated that hydrogen bonds and van der Waals forces played major roles in the binding of LAF to ctDNA. The changes in CD spectra indicated that LAF induced a slight perturbation on the base stacking and helicity of B-DNA. A comparative study of the LAF-ctDNA complex with respect to potassium iodide quenching experiments and competition displacement assays with ethidium bromide, acridine orange, and Hoechst 33258 probes suggested that LAF interacted with ctDNA by minor groove mode. Molecular docking analysis further supported the minor groove binding. Molecular dynamics simulation indicated that LAF depart from the C-G region of DNA, but it can steadily bind with the middle part of DNA composed by A-T base pairs. Copyright © 2017 Elsevier B.V. All rights reserved.
A Dynamic Job Shop Scheduling Method Based on Lagrangian Relaxation
无
1999-01-01
Due to the complexity of dynamic job shop scheduling in flexible manufacturing s ystem(FMS), many heuristic rules are still used today. A dynamic scheduling appr oach based on Lagrangian relaxation is proposed to improve the quality and guara ntee the real-time capability of dynamic scheduling. The proposed method makes use of the dynamic predictive optimal theory combined with Lagrangian relaxation to obtain a good solution that can be evaluated quantitatively. The Lagrangian multipliers introduced here are capable of describing machine predictive states and system capacity constraints. This approach can evaluate the suboptimality of the scheduling systems. It can also quickly obtain high quality feasible schedu les, thus enabling Lagrangian relaxation to be better used in the dynamic schedu ling of manufacturing system. The efficiency and effectiveness of this method ar e verified by numerical experiments.
Collective and molecular relaxation in ferroelectric liquid crystals
Wrobel, S.; Marzec, M.; Godlewska, Malgorzata; Gestblom, B.; Hiller, Steffen; Haase, Wolfgang
1995-08-01
Ferroelectric liquid crystals are molecular ferroelectrics showing up in the tilted liquid crystalline systems (SmC*, SmI*, SmF*) composed of chiral molecules. In this work, we present the dielectric, electro-optic, and calorimetric studies of a single component system: 3-octyloxy-6[2-fluor-4-(2-fluoroctyloxy)phenyl]-pyridine showing interesting ferroelectric properties. The compound exhibits a first order N*- SmC* phase transition which leads to a qualitatively new behavior, for instance the relaxation frequency of the soft mode below TC seems to be temperature independent. The high frequency relaxation process, connected with the reorientation around the long axis, is practically undisturbed at the N*-SmC* transition. Yet, it was found that in the SmC* phase, the best fit was obatined with two Cole-Cole functions yielding two relaxation times to describe a biased reorientation of molecules in the SmC* phase.
Stability and suppression of turbulence in relaxing molecular gas flows
Grigoryev, Yurii N
2017-01-01
This book presents an in-depth systematic investigation of a dissipative effect which manifests itself as the growth of hydrodynamic stability and suppression of turbulence in relaxing molecular gas flows. The work describes the theoretical foundations of a new way to control stability and laminar turbulent transitions in aerodynamic flows. It develops hydrodynamic models for describing thermal nonequilibrium gas flows which allow the consideration of suppression of inviscid acoustic waves in 2D shear flows. Then, nonlinear evolution of large-scale vortices and Kelvin-Helmholtz waves in relaxing shear flows are studied. Critical Reynolds numbers in supersonic Couette flows are calculated analytically and numerically within the framework of both linear and nonlinear classical energy hydrodynamic stability theories. The calculations clearly show that the relaxation process can appreciably delay the laminar-turbulent transition. The aim of the book is to show the new dissipative effect, which can be used for flo...
Relaxation dynamics of amorphous dibucaine using dielectric studies
Sahra, M.; Jumailath, K.; Thayyil, M. Shahin; Capaccioli, S.
2015-06-01
Using broadband dielectric spectroscopy the molecular mobility of dibucaine is investigated in the supercooled liquid and gassy states, over a wide temperature range for some test frequencies. Above the glass transition temperature Tg, the presence of structural α- relaxation peak was observed due to the cooperative motions of the molecule and upon cooling frozen kinetically to form the glass. The secondary relaxation process was perceivable below Tg due to localized motions. The peak loss frequency of α-relaxation process shows non-Arrhenius behavior and obeys Vogel-Fulcher-Tammann equation over the measured temperature range whereas the β- process shows Arrhenius behavior.
Relaxation Dynamics of Non-Power-Law Fluids
Min, Qi; Duan, Yuan-Yuan; Wang, Xiao-Dong; Liang, Zhan-Peng; Lee, Duu-Jong
2013-12-01
The relaxation of non-Newtonian liquids with non-power-law rheology on partially wetted surfaces is rarely investigated. This study assesses the relaxation behavior of 14 partial wetting systems with non-power-law fluids by sessile drop method. These systems are two carboxymethylcellulose sodium solutions on two kinds of slides, cover glass, and silicon wafer surfaces; three polyethylene glycol (PEG400) + silica nanoparticle suspensions on polymethyl methacrylate and polystyrene surfaces. The dynamic contact angle and moving velocity of contact line relationship data for relaxation drops of the 14 tested systems demonstrate a power-law fluid-like behavior, and the equivalent power exponent for a certain fluid on different solid substrates are uniform. By analyzing the relationship between the equivalent power exponent and shear rate, it is proposed that a fluid regime with shear rates of a few tens of s controls relaxation dynamics.
Relaxation Mechanisms in Glassy Dynamics: the Arrhenius and Fragile Regimes
Hentschel, H. George E.; Karmakar, Smarajit; Procaccia, Itamar; Zylberg, Jacques
2012-01-01
Generic glass formers exhibit at least two characteristic changes in their relaxation behavior, first to an Arrhenius-type relaxation at some characteristic temperature, and then at a lower characteristic temperature to a super-Arrhenius (fragile) behavior. We address these transitions by studying the statistics of free energy barriers for different systems at different temperatures and space dimensions. We present a clear evidence for changes in the dynamical behavior at the transition to Ar...
Nonequilibrium molecular dynamics
Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
Glass transition and relaxation dynamics of propylene glycol-water solutions confined in clay
Elamin, Khalid; Björklund, Jimmy; Nyhlén, Fredrik; Yttergren, Madeleine; Mârtensson, Lena; Swenson, Jan
2014-07-01
The molecular dynamics of aqueous solutions of propylene glycol (PG) and propylene glycol methylether (PGME) confined in a two-dimensional layer-structured Na-vermiculite clay has been studied by broadband dielectric spectroscopy and differential scanning calorimetry. As typical for liquids in confined geometries the intensity of the cooperative α-relaxation becomes considerably more suppressed than the more local β-like relaxation processes. In fact, at high water contents the calorimetric glass transition and related structural α-relaxation cannot even be observed, due to the confinement. Thus, the intensity of the viscosity related α-relaxation is dramatically reduced, but its time scale as well as the related glass transition temperature Tg are for both systems only weakly influenced by the confinement. In the case of the PGME-water solutions it is an important finding since in the corresponding bulk system a pronounced non-monotonic concentration dependence of the glass transition related dynamics has been observed due to the growth of hydrogen bonded relaxing entities of water bridging between PGME molecules [J. Sjöström, J. Mattsson, R. Bergman, and J. Swenson, Phys. Chem. B 115, 10013 (2011)]. The present results suggest that the same type of structural entities are formed in the quasi-two-dimensional space between the clay platelets. It is also observed that the main water relaxation cannot be distinguished from the β-relaxation of PG or PGME in the concentration range up to intermediate water contents. This suggests that these two processes are coupled and that the water molecules affect the time scale of the β-relaxation. However, this is most likely true also for the corresponding bulk solutions, which exhibit similar time scales of this combined relaxation process below Tg. Finally, it is found that at higher water contents the water relaxation does not merge with, or follow, the α-relaxation above Tg, but instead crosses the α-relaxation
Relaxation dynamics of a protein solution investigated by dielectric spectroscopy.
Wolf, M; Gulich, R; Lunkenheimer, P; Loidl, A
2012-05-01
In the present work, we provide a dielectric study on two differently concentrated aqueous lysozyme solutions in the frequency range from 1MHz to 40GHz and for temperatures from 275 to 330K. We analyze the three dispersion regions, commonly found in protein solutions, usually termed β-, γ-, and δ-relaxations. The β-relaxation, occurring in the frequency range around 10MHz and the γ-relaxation around 20GHz (at room temperature) can be attributed to the rotation of the polar protein molecules in their aqueous medium and the reorientational motion of the free water molecules, respectively. The nature of the δ-relaxation, which is often ascribed to the motion of bound water molecules, is not yet fully understood. Here we provide data on the temperature dependence of the relaxation times and relaxation strengths of all three detected processes and on the dc conductivity arising from ionic charge transport. The temperature dependences of the β- and γ-relaxations are closely correlated. We found a significant temperature dependence of the dipole moment of the protein, indicating conformational changes. Moreover we find a breakdown of the Debye-Stokes-Einstein relation in this protein solution, i.e., the dc conductivity is not completely governed by the mobility of the solvent molecules. Instead it seems that the dc conductivity is closely connected to the hydration shell dynamics.
Molecular dynamics simulations
Tarmyshov, Konstantin B.
2007-01-01
Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...
Perlík, Václav; Šanda, František
2017-08-01
We present a computational model for the spectra of molecular aggregates with signatures of vibronic progression. Vibronic dynamics is implemented by coupling the dynamics of Frenkel excitons with underdamped vibrations. Vibrational dynamics includes linear damping resulting in the exponential decay and quadratic damping inducing subexponential or power law relaxation and increasing vibrational decoherence as demonstrated on lineshapes of the absorption spectrum. Simulations of the third-order coherent response account for bath reorganization during excitonic transport, which allows us to study the line-shape evolution of cross peaks of 2D spectra.
Dynamics of Sulfonated Polystyrene Ionomers by Dielectric Relaxation Spectroscopy
Castagna, Alicia; Wang, Wenqin; Winey, Karen; Runt, James
2010-03-01
Broadband dielectric spectroscopy was used to investigate the dynamics of sulfonated polystyrene (SPS) ionomers, in both the acid and neutralized form. This study seeks to elucidate the role of counter ion type (Zn, Na, and Cs), degree of sulfonation (9 and 6%), and ion cluster morphology on the relaxation phenomena of SPS. Degree of neutralization and ion type have been found to significantly impact the breadth and time scale of the segmental relaxation process. High temperature relaxation processes, tentatively proposed to arise from Maxwell-Wagner-Sillars interfacial polarization and a hydrogen bonding relaxation, have also been identified. Bands in the sulfonate stretching region of FTIR spectra reveal information about ion coordination in the local aggregate environment. A combination of scanning transmission electron microscopy imaging and X-ray scattering confirmed the presence of homogeneously distributed, nearly monodisperse spherical ionic aggregates in the polymer matrix.
Polymer friction Molecular Dynamics
Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.
We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....
Relaxation mechanisms in glassy dynamics: the Arrhenius and fragile regimes.
Hentschel, H George E; Karmakar, Smarajit; Procaccia, Itamar; Zylberg, Jacques
2012-06-01
Generic glass formers exhibit at least two characteristic changes in their relaxation behavior, first to an Arrhenius-type relaxation at some characteristic temperature and then at a lower characteristic temperature to a super-Arrhenius (fragile) behavior. We address these transitions by studying the statistics of free energy barriers for different systems at different temperatures and space dimensions. We present a clear evidence for changes in the dynamical behavior at the transition to Arrhenius and then to a super-Arrhenius behavior. A simple model is presented, based on the idea of competition between single-particle and cooperative dynamics. We argue that Arrhenius behavior can take place as long as there is enough free volume for the completion of a simple T1 relaxation process. Once free volume is absent one needs a cooperative mechanism to "collect" enough free volume. We show that this model captures all the qualitative behavior observed in simulations throughout the considered temperature range.
Relaxation dynamics in a double-well potential
Cacciari, Ilaria [Istituto di Fisica Applicata ' Nello Carrara' , C.N.R., via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence (Italy)]. E-mail: i.cacciari@ifac.cnr.it; Moretti, Paolo [Istituto dei Sistemi Complessi, C.N.R., Sezione di Firenze, via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence (Italy)]. E-mail: paolo.moretti@isc.cnr.it
2006-10-30
The dynamics of a two-state system subject to coherent tunneling and decay is studied using a simple quantum mechanical model, that can be applied to various physical situations. A satisfactory result, describing the behaviour of the relaxation trajectories, is obtained.
Sastry, V. S. S.; Polimeno, Antonino; Crepeau, Richard H.; Freed, Jack H.
1996-10-01
Two-dimensional Fourier transform (2D-FT) electron spin resonance (ESR) studies on the rigid rodlike cholestane (CSL) spin-label in the liquid crystal solvent 4O,8 (butoxy benzylidene octylaniline) are reported. These experiments were performed over a wide temperature range: 96 °C to 25 °C covering the isotropic (I), nematic (N), smectic A (SA), smectic B (SB), and crystal (C) phases. It is shown that 2D-FT-ESR, especially in the form of 2D-ELDOR (two-dimensional electron-electron double resonance) provides greatly enhanced sensitivity to rotational dynamics than previous cw-ESR studies on this and related systems. This sensitivity is enhanced by obtaining a series of 2D-ELDOR spectra as a function of mixing time, Tm, yielding essentially a three-dimensional experiment. Advantage is taken of this sensitivity to study the applicability of the model of a slowly relaxing local structure (SRLS). In this model, a dynamic cage of solvent molecules, which relaxes on a slower time scale than the CSL solute, provides a local orienting potential in addition to that of the macroscopic aligning potential in the liquid crystalline phase. The theory of Polimeno and Freed for SRLS in the ESR slow motional regime is extended by utilizing the theory of Lee et al. to include 2D-FT-ESR experiments, and it serves as the basis for the analysis of the 2D-ELDOR experiments. It is shown that the SRLS model leads to significantly improved non-linear least squares fits to experiment over those obtained with the standard model of Brownian reorientation in a macroscopic aligning potential. This is most evident for the SA phase, and the use of the SRLS model also removes the necessity of fitting with the unreasonably large CSL rotational asymmetries in the smectic phases that are required in both the cw-ESR and 2D-ELDOR fits with the standard model. The cage potential is found to vary from about kBT in the isotropic phase to greater than 2kBT in the N and SA phases, with an abrupt drop to
Field theory of bicritical and tetracritical points. II. Relaxational dynamics.
Folk, R; Holovatch, Yu; Moser, G
2008-10-01
We calculate the relaxational dynamical critical behavior of systems of O(n_||)(plus sign in circle)O(n_perpendicular) symmetry by renormalization group method within the minimal subtraction scheme in two-loop order. The three different bicritical static universality classes previously found for such systems correspond to three different dynamical universality classes within the static borderlines. The Heisenberg and the biconical fixed point lead to strong dynamic scaling whereas in the region of stability of the decoupled fixed point weak dynamic scaling holds. Due to the neighborhood of the stability border between the strong and the weak scaling dynamic fixed point to the dynamical stable fixed point a very small dynamic transient exponent of omega(Beta)_(v) =0.0044 is present in the dynamics for the physically important case n_|| =1 and n_perpendicular =2 in d=3 .
Sastry, V. S. S.; Polimeno, Antonino; Crepeau, Richard H.; Freed, Jack H.
1996-10-01
Two-dimensional Fourier transform (2D-FT)-electron spin resonance (ESR) studies on the small globular spin probe perdeuterated tempone (PDT) in the liquid crystal solvent 4O,8 (butoxy benzylidene octylaniline) are reported. These experiments, over the temperature range of 95 °C to 24 °C, cover the isotropic (I), nematic (N), smectic A (SA), smectic B (SB), and crystal (C) phases. The 2D-ELDOR (two-dimensional electron-electron double resonance) spectra confirm the anomalously rapid reorientation of PDT, especially in the lower temperature phases. The model of a slowly relaxing local structure (SRLS) leads to generally very good non-linear least squares (NLLS) global fits to the sets of 2D-ELDOR spectra obtained at each temperature. These fits are significantly better than those achieved by the standard model of Brownian reorientation in a macroscopic orienting potential. The SRLS model is able to account for anomalies first observed in an earlier 2D-ELDOR study on PDT in a different liquid crystal in its smectic phases. Although it is instructional to extract the various spectral densities from the COSY (correlation spectroscopy) and 2D-ELDOR spectra, the use of NLLS global fitting to a full set of 2D-ELDOR spectra is shown to be more reliable and convenient for obtaining optimum model parameters, especially in view of possible (incipient) slow motional effects from the SRLS or dynamic cage. The cage potential is found to remain fairly constant at about kBT over the various phases (with only a small drop in the SB phase), but its asymmetry increases with decreasing temperature T. This value is significantly larger than the weak macroscopic orienting potential which increases from 0.1 to 0.3kBT with decreasing T. The cage relaxation rate, given by Rc is about 3×107 s-1 in the I phase, but increases to about 108 s-1 in the SA, SB, and C phases. The rotational diffusion tensor for PDT shows only a small T-independent asymmetry, and its mean rotational diffusion
Substructured multibody molecular dynamics.
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
Tracking ultrafast relaxation dynamics of furan by femtosecond photoelectron imaging
Liu, Yuzhu, E-mail: yuzhu.liu@gmail.com [School of Physics and Optoelectronic Engineering, Nanjing University of Information Science and Technology, Nanjing 210044 (China); Knopp, Gregor [Paul Scherrer Institute, Villigen 5232 (Switzerland); Qin, Chaochao [Department of Physics, Henan Normal University, Xinxiang 453007 (China); Gerber, Thomas [Paul Scherrer Institute, Villigen 5232 (Switzerland)
2015-01-13
Graphical abstract: - Highlights: • Relaxation dynamics of furan are tracked by femtosecond photoelectron imaging. • The mechanism for ultrafast formation of α-carbene and β-carbene is proposed. • Ultrafast internal conversion from S{sub 2} to S{sub 1} is observed. • The transient characteristics of the fragment ions are obtained. • Single-color multi-photon ionization dynamics at 800 nm are also studied. - Abstract: Ultrafast internal conversion dynamics of furan has been studied by femtosecond photoelectron imaging (PEI) coupled with photofragmentation (PF) spectroscopy. Photoelectron imaging of single-color multi-photon ionization and two-color pump–probe ionization are obtained and analyzed. Photoelectron bands are assigned to the related states. The time evolution of the photoelectron signal by pump–probe ionization can be well described by a biexponential decay: two rapid relaxation pathways with time constants of ∼15 fs and 85 (±11) fs. The rapid relaxation is ascribed to the ultrafast internal conversion (IC) from the S{sub 2} state to the vibrationally hot S{sub 1} state. The second relaxation process is attributed to the redistributions and depopulation of secondarily populated high vibronic S{sub 1} state and the formation of α-carbene and β-carbene by H immigration. Additionally, the transient characteristics of the fragment ions are also measured and discussed as a complementary understanding.
Revisiting the relaxation dynamics of isolated pyrrole
Montero, Raúl; Ovejas, Virginia; Fernández-Fernández, Marta; Longarte, Asier, E-mail: asier.longarte@ehu.es [Departamento de Química Física, Universidad del País Vasco (UPV/EHU), Apart. 644, 48080 Bilbao (Spain); Peralta Conde, Álvaro [Centro de Láseres Pulsados (CLPU), Edificio M3, Parque Científico, 37185 Villamayor (Spain)
2014-07-07
Herein, the interpretation of the femtosecond-scale temporal evolution of the pyrrole ion signal, after excitation in the 267–217 nm interval, recently published by our group [R. Montero, A. Peralta Conde, V. Ovejas, M. Fernández-Fernández, F. Castaño, J. R. Vázquez de Aldana, and A. Longarte, J. Chem. Phys.137, 064317 (2012)] is re-visited. The observation of a shift in the pyrrole{sup +} transient respect to zero delay reference, initially attributed to ultrafast dynamics on the πσ{sup *} type state (3s a{sub 1} ← π 1a{sub 2}), is demonstrated to be caused by the existence of pump + probe populated states, along the ionization process. The influence of these resonances in pump-prone ionization experiments, when multi-photon probes are used, and the significance of a proper zero-time reference, is discussed. The possibility of preparing the πσ{sup *} state by direct excitation is investigated by collecting 1 + 1 photoelectron spectra, at excitation wavelengths ranging from 255 to 219 nm. No conclusive evidences of ionization through this state are found.
Automatically Discovering Relaxed Lyapunov Functions for Polynomial Dynamical Systems
Liu, Jiang; Zhao, Hengjun
2011-01-01
The notion of Lyapunov function plays a key role in design and verification of dynamical systems, as well as hybrid and cyber-physical systems. In this paper, to analyze the asymptotic stability of a dynamical system, we generalize standard Lyapunov functions to relaxed Lyapunov functions (RLFs), by considering higher order Lie derivatives of certain functions along the system's vector field. Furthermore, we present a complete method to automatically discovering polynomial RLFs for polynomial dynamical systems (PDSs). Our method is complete in the sense that it is able to discover all polynomial RLFs by enumerating all polynomial templates for any PDS.
Soheilifard, Reza; Makarov, Dmitrii E; Rodin, Gregory J
2011-08-07
Reduced-dimensionality, coarse-grained models are commonly employed to describe the structure and dynamics of large molecular systems. In those models, the dynamics is often described by Langevin equations of motion with phenomenological parameters. This paper presents a rigorous coarse-graining method for the dynamics of linear systems. In this method, as usual, the conformational space of the original atomistic system is divided into master and slave degrees of freedom. Under the assumption that the characteristic timescales of the masters are slower than those of the slaves, the method results in Langevin-type equations of motion governed by an effective potential of mean force. In addition, coarse-graining introduces hydrodynamic-like coupling among the masters as well as non-trivial inertial effects. Application of our method to the long-timescale part of the relaxation spectra of proteins shows that such dynamic coupling is essential for reproducing their relaxation rates and modes.
Minecka, Aldona; Kamińska, Ewa; Tarnacka, Magdalena; Dzienia, Andrzej; Madejczyk, Olga; Waliłko, Patrycja; Kasprzycka, Anna; Kamiński, Kamil; Paluch, Marian
2017-08-01
In this paper, broadband dielectric spectroscopy was applied to investigate molecular dynamics of 1,2,3,4,6-penta-O-(trimethylsilyl)-D-glucopyranose (S-GLU) at ambient and elevated pressures. Our studies showed that apart from the structural relaxation, one well resolved asymmetric secondary process (initially labeled as β) is observed in the spectra measured at p = 0.1 MPa. Analysis with the use of the coupling model and criterion proposed by Ngai and Capaccioli indicated that the β-process in S-GLU is probably a Johari-Goldstein relaxation of intermolecular origin. Further high pressure experiments demonstrated that there are in fact two secondary processes contributing to the β-relaxation. Therefore, one can postulate that the coupling model is a necessary, but not sufficient criterion to identify the true nature of the given secondary relaxation process. The role of pressure experiments in better understanding of the molecular origin of local mobility seems to be much more important. Interestingly, our research also revealed that the structural relaxation in S-GLU is very sensitive to compression. It was reflected in an extremely high pressure coefficient of the glass transition temperature (dTg/dp = 412 K/GPa). According to the literature data, such a high value of dTg/dp has not been obtained so far for any H-bonded, van der Waals, or polymeric glass-formers.
Arrested relaxation in an isolated molecular ultracold plasma
Haenel, R.; Schulz-Weiling, M.; Sous, J.; Sadeghi, H.; Aghigh, M.; Melo, L.; Keller, J. S.; Grant, E. R.
2017-08-01
Spontaneous avalanche to plasma splits the core of an ellipsoidal Rydberg gas of nitric oxide. Ambipolar expansion first quenches the electron temperature of this core plasma. Then, long-range, resonant charge transfer from ballistic ions to frozen Rydberg molecules in the wings of the ellipsoid quenches the ion-Rydberg-molecule relative velocity distribution. This sequence of steps gives rise to a remarkable mechanics of self-assembly, in which the kinetic energy of initially formed hot electrons and ions drives an observed separation of plasma volumes. These dynamics adiabatically sequester energy in a reservoir of mass transport, starting a process that anneals separating volumes to form an apparent glass of strongly coupled ions and electrons. Short-time electron spectroscopy provides experimental evidence for complete ionization. The long lifetime of this system, particularly its stability with respect to recombination and neutral dissociation, suggests that this transformation affords a robust state of arrested relaxation, far from thermal equilibrium.
Molecular Scale Dynamics of Large Ring Polymers
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.
Numerical modeling of bubble dynamics in viscoelastic media with relaxation
Warnez, M. T.; Johnsen, E.
2015-06-01
Cavitation occurs in a variety of non-Newtonian fluids and viscoelastic materials. The large-amplitude volumetric oscillations of cavitation bubbles give rise to high temperatures and pressures at collapse, as well as induce large and rapid deformation of the surroundings. In this work, we develop a comprehensive numerical framework for spherical bubble dynamics in isotropic media obeying a wide range of viscoelastic constitutive relationships. Our numerical approach solves the compressible Keller-Miksis equation with full thermal effects (inside and outside the bubble) when coupled to a highly generalized constitutive relationship (which allows Newtonian, Kelvin-Voigt, Zener, linear Maxwell, upper-convected Maxwell, Jeffreys, Oldroyd-B, Giesekus, and Phan-Thien-Tanner models). For the latter two models, partial differential equations (PDEs) must be solved in the surrounding medium; for the remaining models, we show that the PDEs can be reduced to ordinary differential equations. To solve the general constitutive PDEs, we present a Chebyshev spectral collocation method, which is robust even for violent collapse. Combining this numerical approach with theoretical analysis, we simulate bubble dynamics in various viscoelastic media to determine the impact of relaxation time, a constitutive parameter, on the associated physics. Relaxation time is found to increase bubble growth and permit rebounds driven purely by residual stresses in the surroundings. Different regimes of oscillations occur depending on the relaxation time.
Generalized dynamic scaling for quantum critical relaxation in imaginary time.
Zhang, Shuyi; Yin, Shuai; Zhong, Fan
2014-10-01
We study the imaginary-time relaxation critical dynamics of a quantum system with a vanishing initial correlation length and an arbitrary initial order parameter M0. We find that in quantum critical dynamics, the behavior of M0 under scale transformations deviates from a simple power law, which was proposed for very small M0 previously. A universal characteristic function is then suggested to describe the rescaled initial magnetization, similar to classical critical dynamics. This characteristic function is shown to be able to describe the quantum critical dynamics in both short- and long-time stages of the evolution. The one-dimensional transverse-field Ising model is employed to numerically determine the specific form of the characteristic function. We demonstrate that it is applicable as long as the system is in the vicinity of the quantum critical point. The universality of the characteristic function is confirmed by numerical simulations of models belonging to the same universality class.
Viscosity, relaxation time, and dynamics within a model asphalt of larger molecules
Li, Derek D.; Greenfield, Michael L.
2014-01-01
The dynamics properties of a new "next generation" model asphalt system that represents SHRP AAA-1 asphalt using larger molecules than past models is studied using molecular simulation. The system contains 72 molecules distributed over 12 molecule types that range from nonpolar branched alkanes to polar resins and asphaltenes. Molecular weights range from 290 to 890 g/mol. All-atom molecular dynamics simulations conducted at six temperatures from 298.15 to 533.15 K provide a wealth of correlation data. The modified Kohlrausch-Williams-Watts equation was regressed to reorientation time correlation functions and extrapolated to calculate average rotational relaxation times for individual molecules. The rotational relaxation rate of molecules decreased significantly with increasing size and decreasing temperature. Translational self-diffusion coefficients followed an Arrhenius dependence. Similar activation energies of ˜42 kJ/mol were found for all 12 molecules in the model system, while diffusion prefactors spanned an order of magnitude. Viscosities calculated directly at 533.15 K and estimated at lower temperatures using the Debye-Stokes-Einstein relationship were consistent with experimental data for asphalts. The product of diffusion coefficient and rotational relaxation time showed only small changes with temperature above 358.15 K, indicating rotation and translation that couple self-consistently with viscosity. At lower temperatures, rotation slowed more than diffusion.
Viscosity, relaxation time, and dynamics within a model asphalt of larger molecules
Li, Derek D.; Greenfield, Michael L., E-mail: greenfield@egr.uri.edu [Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881 (United States)
2014-01-21
The dynamics properties of a new “next generation” model asphalt system that represents SHRP AAA-1 asphalt using larger molecules than past models is studied using molecular simulation. The system contains 72 molecules distributed over 12 molecule types that range from nonpolar branched alkanes to polar resins and asphaltenes. Molecular weights range from 290 to 890 g/mol. All-atom molecular dynamics simulations conducted at six temperatures from 298.15 to 533.15 K provide a wealth of correlation data. The modified Kohlrausch-Williams-Watts equation was regressed to reorientation time correlation functions and extrapolated to calculate average rotational relaxation times for individual molecules. The rotational relaxation rate of molecules decreased significantly with increasing size and decreasing temperature. Translational self-diffusion coefficients followed an Arrhenius dependence. Similar activation energies of ∼42 kJ/mol were found for all 12 molecules in the model system, while diffusion prefactors spanned an order of magnitude. Viscosities calculated directly at 533.15 K and estimated at lower temperatures using the Debye-Stokes-Einstein relationship were consistent with experimental data for asphalts. The product of diffusion coefficient and rotational relaxation time showed only small changes with temperature above 358.15 K, indicating rotation and translation that couple self-consistently with viscosity. At lower temperatures, rotation slowed more than diffusion.
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
Collective Relaxation Dynamics of Small-World Networks
Grabow, Carsten; Kurths, Jürgen; Timme, Marc
2015-01-01
Complex networks exhibit a wide range of collective dynamic phenomena, including synchronization, diffusion, relaxation, and coordination processes. Their asymptotic dynamics is generically characterized by the local Jacobian, graph Laplacian or a similar linear operator. The structure of networks with regular, small-world and random connectivities are reasonably well understood, but their collective dynamical properties remain largely unknown. Here we present a two-stage mean-field theory to derive analytic expressions for network spectra. A single formula covers the spectrum from regular via small-world to strongly randomized topologies in Watts-Strogatz networks, explaining the simultaneous dependencies on network size N, average degree k and topological randomness q. We present simplified analytic predictions for the second largest and smallest eigenvalue, and numerical checks confirm our theoretical predictions for zero, small and moderate topological randomness q, including the entire small-world regime...
Theoretical Studies of the Relaxation Matrix for Molecular Systems
Ma, Qiancheng; Boulet, C.
2016-06-01
The phenomenon of collisional transfer of intensity due to line mixing has an increasing importance for atmospheric monitoring. From a theoretical point of view, all relevant information about the collisional processes is contained in the relaxation matrix where the diagonal elements give half-widths and shifts, and the off-diagonal elements correspond to line interferences. For simple systems such as those consisting of diatom-atom or diatom-diatom, accurate fully quantum calculations based on interaction potentials are feasible. However, fully quantum calculations become unrealistic for more complex systems. On the other hand, the semi-classical Robert-Bonamy formalism, which has been widely used to calculate half-widths and shifts for decades, fails in calculating the off-diagonal matrix elements resulting from applying the isolated line approximation. As a result, in order to simulate atmospheric spectra where the effects from line mixing are important, semi-empirical fitting or scaling laws such as the energy corrected sudden (ECS) and the infinite order sudden (IOS) models are commonly used. Recently, we have found that in developing this semi-classical line shape theory, to rely on the isolated line approximation is not necessary. By eliminating this unjustified assumption, and accurately evaluating matrix elements of the exponential operators, we have developed a more capable formalism that enables one not only to reduce uncertainties for calculated half-widths and shifts, but also to calculate the whole relaxation matrix. This implies that we can address the line mixing with the semi-classical theory based on interaction potentials between molecular absorber and molecular perturber. We have applied this formalism for Raman and infrared spectra of linear and asymmetric-top molecules. Recently, the method has been extended into symmetric-tops with inverse symmetry such as the NH3 molecule. Our calculated half-widths of NH3 lines in the νb{1} and the pure
Universal nonexponential relaxation: Complex dynamics in simple liquids.
Turton, David A; Wynne, Klaas
2009-11-28
The dynamics of the noble-gas liquids underlies that of all liquids making them an important prototypical model system. Using optical Kerr-effect spectroscopy we show that for argon, krypton, and xenon, both the librational and diffusional contributions to the spectrum are surprisingly complex. The diffusional relaxation appears as a stretched-exponential, such as widely found in studies of structured (e.g., glass-forming) liquids and as predicted by mode-coupling theory. We show that this behavior is remarkably similar to that measured in water and suggest that it is a fundamental or universal property.
The short-time intramolecular dynamics of solutes in liquids. II. Vibrational population relaxation
Goodyear, Grant; Stratt, Richard M.
1997-08-01
Events such as the vibrational relaxation of a solute are often well described by writing an effective equation of motion—a generalized Langevin equation—which expresses the surrounding medium's influence on the intramolecular dynamics in terms of a friction and a fluctuating force acting on the solute. These quantities, though, can be obtained from the instantaneous normal modes (INMs) of the system when the relaxation takes place in a fluid, suggesting that we should be able to analyze in some detail the solvent motions driving the relaxation, at least for short times. In this paper we show that this promise can indeed be realized for the specific case of a vibrating diatomic molecule dissolved in an atomic solvent. Despite the relatively long times typical of vibrational population relaxation, it turns out that understanding the behavior of the vibrational friction at the short times appropriate to INMs (a few hundred femtoseconds) often suffices to predict T1 times. We use this observation to probe the dependence of these relaxation rates on thermodynamic conditions and to look at the molecular mechanisms underlying the process. We find that raising the temperature at any given density or raising the density at any given temperature will invariably increase the rate of energy relaxation. However, since these two trends may be in conflict in a typical constant-pressure laboratory experiment, we also find that it is possible to make sense of the "anomalous" inverted temperature dependence recently seen experimentally. We find, as well, that the INM theory—which has no explicit collisions built into it—predicts exactly the same density dependence as the venerable independent-binary-collision (IBC) theory (an intriguing result in view of recent claims that experimental observations of this kind of dependence provide support for the IBC theory). The actual mechanisms behind vibrational population relaxation are revealed by looking in detail at the
Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)
2015-12-14
In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.
Vibrational relaxation and vibrational cooling in low temperature molecular crystals
Hill, Jeffrey R.; Chronister, Eric L.; Chang, Ta-Chau; Kim, Hackjin; Postlewaite, Jay C.; Dlott, Dana D.
1988-01-01
The processes of vibrational relaxation (VR) and vibrational cooling (VC) are investigated in low temperature crystals of complex molecules, specifically benzene, naphthalene, anthracene, and durene. In the VR process, a vibration is deexcited, while VC consists of many sequential and parallel VR steps which return the crystal to thermal equilibrium. A theoretical model is developed which relates the VR rate to the excess vibrational energy, the molecular structure, and the crystal structure. Specific relations are derived for the vibrational lifetime T1 in each of three regimes of excess vibrational energy. The regimes are the following: Low frequency regime I where VR occurs by emission of two phonons, intermediate frequency regime II where VR occurs by emission of one phonon and one vibration, and high frequency regime III where VR occurs by evolution into a dense bath of vibrational combinations. The VR rate in each regime depends on a particular multiphonon density of states and a few averaged anharmonic coefficients. The appropriate densities of states are calculated from spectroscopic data, and together with available VR data and new infrared and ps Raman data, the values of the anharmonic coefficients are determined for each material. The relationship between these parameters and the material properties is discussed. We then describe VC in a master equation formalism. The transition rate matrix for naphthalene is found using the empirically determined parameters of the above model, and the time dependent redistribution in each mode is calculated.
Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.
Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J; Suchard, Marc A; Lemey, Philippe
2013-02-01
Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike's information criterion through Markov chain Monte Carlo (AICM), in bayesian model selection of demographic and molecular clock models. Almost simultaneously, a bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets.
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Inhibited, Explosive and Anisotropic Relaxation in a Gas of Molecular Super-Rotors
Khodorkovsky, Yuri; Hartmann, Jean-Michel; Averbukh, Ilya Sh
2015-01-01
Recently, several femtosecond laser techniques have been developed that are capable of bringing gas molecules to extremely fast rotation in a very short time, while keeping their translational motion intact and relatively slow. We investigate collisional equilibration dynamics of this new state of molecular gases, and find that it follows a remarkable generic scenario. The route to equilibrium starts with a durable metastable 'gyroscopic stage', in the course of which the molecules maintain their fast rotation and orientation of the angular momentum through many collisions. The inhibited rotational-translational relaxation is characterized by a persistent anisotropy in the molecular angular distribution, and is manifested in the long-lasting optical birefringence, and anisotropic diffusion in the gas. After a certain induction time, the 'gyroscopic stage' is abruptly terminated by a self-accelerating explosive rotational-translational energy exchange leading the gas towards the final thermal equilibrium. We i...
Molecular Dynamics and Protein Function
M. Karplus; J. Kuriyan; Bruce J. Berne
2005-01-01
.... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...
Picosecond Dynamic Heterogeneity, Hopping, and Johari-Goldstein Relaxation in Glass-Forming Liquids
Cicerone, Marcus T.; Zhong, Qin; Tyagi, Madhusudan
2014-09-01
We show that incoherent quasielastic neutron scattering from molecular liquids reveals a two-state dynamic heterogeneity on a 1 ps time scale, where molecules are either highly confined or are free to undergo relatively large excursions. Data ranging from deep in the glassy state to well above the melting point allows us to observe temperature-dependent population levels and exchange between these two states. A simple physical picture emerges from this data, combined with published work, that provides a mechanism for hopping and for the Johari-Goldstein (βJG) relaxation, and allows us to accurately calculate the diffusion coefficient, DT, and characteristic times for α, and βJG relaxations from ps time scale neutron data.
Dynamic nuclear polarization and relaxation of H and D atoms in solid mixtures of hydrogen isotopes
Sheludiakov, S; Järvinen, J; Vainio, O; Lehtonen, L; Vasiliev, S; Lee, D M; Khmelenko, V V
2016-01-01
We report on a study of Dynamic Nuclear Polarization and electron and nuclear spin relaxation of atomic hydrogen and deuterium in solid molecular matrices of H$_{2}$, D$_{2}$, and HD mixtures. The electron and nuclear spin relaxation times ($T_{1e}$ and $T_{1N}$) were measured within the temperature range 0.15-2.5$\\,$K in a magnetic field of 4.6 T, conditions which ensure a high polarization of electron spins. We found that $T_{1e}$ is nearly temperature independent in this temperature range, while $T_{1N}$ decreased by 2 orders of magnitude. Such strong temperature dependence is typical for the nuclear Orbach mechanism of relaxation via the electron spins. We found that the nuclear spins of H atoms in solid D$_{2}$ and D$_{2}:$HD can be efficiently polarized by the Overhauser effect. Pumping the forbidden transitions of H atoms also leads to DNP, with the efficiency strongly dependent on the concentration of D atoms. This behaviour indicates the Cross effect mechanism of the DNP and nuclear relaxation, which...
Open quantum system parameters from molecular dynamics
Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander
2015-01-01
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...
Dielectric relaxation in ionic liquid/dipolar solvent binary mixtures: A semi-molecular theory
Daschakraborty, Snehasis; Biswas, Ranjit
2016-03-01
A semi-molecular theory is developed here for studying dielectric relaxation (DR) in binary mixtures of ionic liquids (ILs) with common dipolar solvents. Effects of ion translation on DR time scale, and those of ion rotation on conductivity relaxation time scale are explored. Two different models for the theoretical calculations have been considered: (i) separate medium approach, where molecularities of both the IL and dipolar solvent molecules are retained, and (ii) effective medium approach, where the added dipolar solvent molecules are assumed to combine with the dipolar ions of the IL, producing a fictitious effective medium characterized via effective dipole moment, density, and diameter. Semi-molecular expressions for the diffusive DR times have been derived which incorporates the effects of wavenumber dependent orientational static correlations, ion dynamic structure factors, and ion translation. Subsequently, the theory has been applied to the binary mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim][BF4]) with water (H2O), and acetonitrile (CH3CN) for which experimental DR data are available. On comparison, predicted DR time scales show close agreement with the measured DR times at low IL mole fractions (xIL). At higher IL concentrations (xIL > 0.05), the theory over-estimates the relaxation times and increasingly deviates from the measurements with xIL, deviation being the maximum for the neat IL by almost two orders of magnitude. The theory predicts negligible contributions to this deviation from the xIL dependent collective orientational static correlations. The drastic difference between DR time scales for IL/solvent mixtures from theory and experiments arises primarily due to the use of the actual molecular volume ( Vmol dip ) for the rotating dipolar moiety in the present theory and suggests that only a fraction of Vmol dip is involved at high xIL. Expectedly, nice agreement between theory and experiments appears when experimental
Dielectric relaxation in ionic liquid/dipolar solvent binary mixtures: A semi-molecular theory.
Daschakraborty, Snehasis; Biswas, Ranjit
2016-03-14
A semi-molecular theory is developed here for studying dielectric relaxation (DR) in binary mixtures of ionic liquids (ILs) with common dipolar solvents. Effects of ion translation on DR time scale, and those of ion rotation on conductivity relaxation time scale are explored. Two different models for the theoretical calculations have been considered: (i) separate medium approach, where molecularities of both the IL and dipolar solvent molecules are retained, and (ii) effective medium approach, where the added dipolar solvent molecules are assumed to combine with the dipolar ions of the IL, producing a fictitious effective medium characterized via effective dipole moment, density, and diameter. Semi-molecular expressions for the diffusive DR times have been derived which incorporates the effects of wavenumber dependent orientational static correlations, ion dynamic structure factors, and ion translation. Subsequently, the theory has been applied to the binary mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim][BF4]) with water (H2O), and acetonitrile (CH3CN) for which experimental DR data are available. On comparison, predicted DR time scales show close agreement with the measured DR times at low IL mole fractions (x(IL)). At higher IL concentrations (x(IL) > 0.05), the theory over-estimates the relaxation times and increasingly deviates from the measurements with x(IL), deviation being the maximum for the neat IL by almost two orders of magnitude. The theory predicts negligible contributions to this deviation from the x(IL) dependent collective orientational static correlations. The drastic difference between DR time scales for IL/solvent mixtures from theory and experiments arises primarily due to the use of the actual molecular volume (V(mol)(dip)) for the rotating dipolar moiety in the present theory and suggests that only a fraction of V(mol)(dip) is involved at high x(IL). Expectedly, nice agreement between theory and experiments appears when
Molecular Exchange Dynamics in Block Copolymer Micelles
Bates, Frank; Lu, Jie; Choi, Soohyung; Lodge, Timothy
2012-02-01
Poly(styrene-b-ethylene propylene) (PS-PEP) diblock copolymers were mixed with squalane (C30H62) at 1% by weight resulting in the formation of spherical micelles. The structure and dynamics of molecular exchange were characterized by synchrotron small-angle x-ray scattering (SAXS) and time resolved small-angle neutron scattering (TR-SANS), respectively, between 100 C and 160 C. TR-SANS measurements were performed with solutions initially containing deuterium labeled micelle cores and normal cores dispersed in a contrast matched squalane. Monitoring the reduction in scattering intensity as a function of time at various temperatures revealed molecular exchange dynamics highly sensitive to the core molecular weight and molecular weight distribution. Time-temperature superposition of data acquired at different temperatures produced a single master curve for all the mixtures. Experiments conducted with isotopically labeled micelle cores, each formed from two different but relatively mondisperse PS blocks, confirmed a simple dynamical model based on first order kinetics and core Rouse single chain relaxation. These findings demonstrate a dramatic transition to nonergodicity with increasing micelle core molecular weight and confirm the origins of the logarithmic exchange kinetics in such systems.
Molecular Dynamics of Lipid Bilayers
1989-08-09
The aim of this work is to study, by molecular dynamics simulations, the properties of lipid bilayers. We have applied the vectorizable, order-N...fast angle-dependent force/potential algorithms to treat angle bending and torsion. Keywords: Molecular dynamics , Lipid bilayers.
Ramos, Joaquim J Moura; Diogo, Hermínio P
2016-03-30
The slow molecular mobility of three active pharmaceutical drugs (voriconazole, miconazole and itraconazole) has been studied by differential scanning calorimetry (DSC) and thermally stimulated depolarization currents (TSDC). This study yielded the main kinetic features of the secondary relaxations and of the main (glass transition) relaxation, in particular their distribution of relaxation times. The dynamic fragility of the three glass formers was determined from DSC data (using two different procedures) and from TSDC data. According to our results voriconazole behaves as a relatively strong liquid, while miconazole is moderately fragile and itraconazole is a very fragile liquid. There are no studies in this area published in the literature relating to voriconazole. Also not available in the literature is a slow mobility study by dielectric relaxation spectroscopy in the amorphous miconazole. Apart from that, the results obtained are in reasonable agreement with published works using different experimental techniques. Copyright © 2016 Elsevier B.V. All rights reserved.
Phase transitions and relaxation dynamics of Ising models exchanging particles
Goh, Segun; Fortin, Jean-Yves; Choi, M. Y.
2017-01-01
A variety of systems in nature and in society are open and subject to exchanging their constituents with other systems (e.g., environments). For instance, in biological systems, cells collect necessary energy and material by exchange of molecules or ions. Similarly, countries, cities or research institutes evolve as their constituents move in or out. To probe the corresponding particle exchange dynamics in such systems, we consider two Ising models exchanging particles and establish a master equation describing the equilibrium phases as well as the non-equilibrium dynamics of the system. It is found that an additional stable phase emerges as a consequence of the particle exchange process. Furthermore, we formulate the Ginzburg-Landau theory which allows to probe correlation effects. Accordingly, critical slowing down is manifested and the associated dynamic exponent is computed in the linear relaxation regime. In particular, this approach is relevant for investigating the grand canonical description of the system plus environment, with particle exchange and state transitions taken into account explicitly.
MDplot: Visualise Molecular Dynamics.
Margreitter, Christian; Oostenbrink, Chris
2017-05-10
The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.
A quantum molecular dynamics study of aqueous solvation dynamics
Videla, Pablo E.; Rossky, Peter J.; Laria, D.
2013-10-01
Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.
Prompers, J J; Brüschweiler, R
2001-08-01
An approach is presented for the interpretation of heteronuclear NMR spin relaxation data in mobile protein parts in terms of reorientational eigenmode dynamics. The method is based on the covariance matrix of the spatial functions of the nuclear spin interactions that cause relaxation expressed as spherical harmonics of rank 2. The approach was applied to characterize the dynamics of a loop region of ubiquitin. The covariance matrix was determined from a conformational ensemble generated by a 5 ns molecular dynamics simulation. It was found that the time correlation functions of the dominant eigenmodes decay in good approximation with a single correlation time. From the reorientational eigenmodes, their eigenvalues, and correlation times, NMR relaxation data were calculated in accordance with Bloch-Wangsness-Redfield relaxation theory and directly compared with experimental (15)N relaxation parameters. Using a fitting procedure, agreement between calculated and experimental data was improved significantly by adjusting eigenvalues and correlation times of the dominant modes. The presented procedure provides detailed information on correlated reorientational dynamics of flexible parts in globular proteins. The covariance matrix was linked to the covariance matrix of backbone dihedral angle fluctuations, allowing one to study the motional behavior of these degrees of freedom on nano- and subnanosecond time scales.
Uranga-Piña, L. [Facultad de Física, Universidad de la Habana, San Lázaro y L, Vedado, 10400 Havana (Cuba); Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, D-14195 Berlin (Germany); Tremblay, J. C., E-mail: jean.c.tremblay@gmail.com [Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, D-14195 Berlin (Germany)
2014-08-21
We investigate the effect of inter-mode coupling on the vibrational relaxation dynamics of molecules in weak dissipative environments. The simulations are performed within the reduced density matrix formalism in the Markovian regime, assuming a Lindblad form for the system-bath interaction. The prototypical two-dimensional model system representing two CO molecules approaching a Cu(100) surface is adapted from an ab initio potential, while the diatom-diatom vibrational coupling strength is systematically varied. In the weak system-bath coupling limit and at low temperatures, only first order non-adiabatic uni-modal coupling terms contribute to surface-mediated vibrational relaxation. Since dissipative dynamics is non-unitary, the choice of representation will affect the evolution of the reduced density matrix. Two alternative representations for computing the relaxation rates and the associated operators are thus compared: the fully coupled spectral basis, and a factorizable ansatz. The former is well-established and serves as a benchmark for the solution of Liouville-von Neumann equation. In the latter, a contracted grid basis of potential-optimized discrete variable representation is tailored to incorporate most of the inter-mode coupling, while the Lindblad operators are represented as tensor products of one-dimensional operators, for consistency. This procedure results in a marked reduction of the grid size and in a much more advantageous scaling of the computational cost with respect to the increase of the dimensionality of the system. The factorizable method is found to provide an accurate description of the dissipative quantum dynamics of the model system, specifically of the time evolution of the state populations and of the probability density distribution of the molecular wave packet. The influence of intra-molecular vibrational energy redistribution appears to be properly taken into account by the new model on the whole range of coupling strengths. It
Uranga-Piña, L; Tremblay, J C
2014-08-21
We investigate the effect of inter-mode coupling on the vibrational relaxation dynamics of molecules in weak dissipative environments. The simulations are performed within the reduced density matrix formalism in the Markovian regime, assuming a Lindblad form for the system-bath interaction. The prototypical two-dimensional model system representing two CO molecules approaching a Cu(100) surface is adapted from an ab initio potential, while the diatom-diatom vibrational coupling strength is systematically varied. In the weak system-bath coupling limit and at low temperatures, only first order non-adiabatic uni-modal coupling terms contribute to surface-mediated vibrational relaxation. Since dissipative dynamics is non-unitary, the choice of representation will affect the evolution of the reduced density matrix. Two alternative representations for computing the relaxation rates and the associated operators are thus compared: the fully coupled spectral basis, and a factorizable ansatz. The former is well-established and serves as a benchmark for the solution of Liouville-von Neumann equation. In the latter, a contracted grid basis of potential-optimized discrete variable representation is tailored to incorporate most of the inter-mode coupling, while the Lindblad operators are represented as tensor products of one-dimensional operators, for consistency. This procedure results in a marked reduction of the grid size and in a much more advantageous scaling of the computational cost with respect to the increase of the dimensionality of the system. The factorizable method is found to provide an accurate description of the dissipative quantum dynamics of the model system, specifically of the time evolution of the state populations and of the probability density distribution of the molecular wave packet. The influence of intra-molecular vibrational energy redistribution appears to be properly taken into account by the new model on the whole range of coupling strengths. It
Schammé, Benjamin; Mignot, Mélanie; Couvrat, Nicolas; Tognetti, Vincent; Joubert, Laurent; Dupray, Valérie; Delbreilh, Laurent; Dargent, Eric; Coquerel, Gérard
2016-08-04
In this article, we conduct a comprehensive molecular relaxation study of amorphous Quinidine above and below the glass-transition temperature (Tg) through broadband dielectric relaxation spectroscopy (BDS) experiments and theoretical density functional theory (DFT) calculations, as one major issue with the amorphous state of pharmaceuticals is life expectancy. These techniques enabled us to determine what kind of molecular motions are responsible, or not, for the devitrification of Quinidine. Parameters describing the complex molecular dynamics of amorphous Quinidine, such as Tg, the width of the α relaxation (βKWW), the temperature dependence of α-relaxation times (τα), the fragility index (m), and the apparent activation energy of secondary γ relaxation (Ea-γ), were characterized. Above Tg (> 60 °C), a medium degree of nonexponentiality (βKWW = 0.5) was evidenced. An intermediate value of the fragility index (m = 86) enabled us to consider Quinidine as a glass former of medium fragility. Below Tg (origin coming from the rotation of the CH(OH)C9H14N end group. An excess wing observed in amorphous Quinidine was found to be an unresolved Johari-Goldstein relaxation. These studies were supplemented by sub-Tg experimental evaluations of the life expectancy of amorphous Quinidine by X-ray powder diffraction and differential scanning calorimetry. We show that the difference between Tg and the onset temperature for crystallization, Tc, which is 30 K, is sufficiently large to avoid recrystallization of amorphous Quinidine during 16 months of storage under ambient conditions.
A method to simulate multilayer welding process: Node dynamic relaxation method
Gao Jiashuang; Yang Jianguo; Fang Hongyuan; Hu Junfeng; Wang Tao
2009-01-01
A new method called node dynamic relaxation is proposed to simulate multilayer welding. A two dimensional plane strain model for multilayer welding is simulated and the results show that mesh distortion can be decreased, and it is also found that the node dynamic relaxation is a kind of method to calculate welding deformation accurately by comparing experiment results with simulation results.
Soliton driven relaxation dynamics and universality in protein collapse
Krokhotin, Andrey; Niemi, Antti J
2011-01-01
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that are based on atomic scale scrutiny. Here we consider an effective dynamical Landau theory to model the folding process at biologically relevant time and distance scales. We reach both a substantial decrease in the execution time and improvement in the accuracy of the final configuration, in comparison to more conventional approaches. As an example we inspect the collapse of HP35 chicken villin headpiece subdomain, where there are detailed molecular dynamics simulations to compare with. We start from a structureless, unbend and untwisted initial configuration. In less than one second of wall-clock time on a single processor personal computer we consistently reach the native state with 0.5 Angstrom root mean square distance (RMSD) precision. We confirm that our folding pathways...
Violent Relaxation, Dynamical Instabilities and the Formation of Elliptical Galaxies
Aguilar, L. A.
1990-11-01
RESUMEN: El problema de la formaci6n de galaxias elfpticas por medjo de colapso gravitacional sin disipaci6n de energfa es estudiado usando un gran numero de simulaciones numericas. Se muestra que este tipo de colapsos, partiendo de condiciones iniciales frfas donde la energfa cinetica inicial representa s6lo un 5%, 0 , de a potencial inicial, produce sistemas relajados de forma triaxial muy similares a las galaxias elfpticas reales en sus formas y perfiles de densidad en proyecci6i . La forina triaxial resulta de la acci6n de una inestabilidad dinamica que aparece en sistemas 'inicos dominados por movimientos radiales, mientras que el perfil de densidad final Cs debido al llamado relajamiento violento que tiende a producir una distribuci6n en espacio fase unica. Estos dos fen6menos tienden a borrar los detalles particulares sobre las condiciones iniciales y dan lugar a una evoluci6n convergente hacia sistemas realistas, esto innecesario el uso de condiciones iniciales especiales (excepto por Ia condici6i de que estas deben ser frfas). Las condiciones iniciales frfas producen los movimientos radiales y fluctuaciones de la energfa potencial requeridos por ambos fen6menos. ABSTRACT: The problem of formation of elliptical galaxies via dissipationless collapse is studied using a large set of numerical simulations. It is shown that dissipationless collapses from cold initial conditions, where the total initial kinetic energy is less than 5% ofthe initial potential energy, lead to relaxed triaxial systems ery similar to real elliptical galaxies ii projected shape and density profiles. The triaxial shape is due to the of a dynamical instability that appears on systems dominated by radial orbits, while final density profile is due to violent relaxation that tends to produce a unique distribution iii space. These two phenomena erase memory of the initial prodtice a convergent evolution toward realistic systems, thus making unnecessary use o[special initial conditions (other
Adrjanowicz, Karolina; Kaminski, Kamil; Paluch, Marian
2015-01-01
In this paper, we study crystallization behavior and molecular dynamics in the supercooled liquid state of the pharmaceutically important compound ketoprofen at various thermodynamic conditions. Dielectric relaxation for a racemic mixture was investigated in a wide range of temperatures and press......In this paper, we study crystallization behavior and molecular dynamics in the supercooled liquid state of the pharmaceutically important compound ketoprofen at various thermodynamic conditions. Dielectric relaxation for a racemic mixture was investigated in a wide range of temperatures...... of pure enantiomers and their 50–50 equimolar mixture in the metastable supercooled liquid state. Crystallization kinetic studies revealed that at the same isochronal conditions the behavior of the S-enantiomer and R,S-racemic mixture of ketoprofen is entirely different. This was examined in the context...
Molecular dynamics of silicon indentation
Kallman, J.S.; Hoover, W.G.; Hoover, C.G.; De Groot, A.J.; Lee, S.M.; Wooten, F. (Department of Applied Science Davis-Livermore, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States))
1993-04-01
We use nonequilibrium molecular dynamics to simulate the elastic-plastic deformation of silicon under tetrahedral nanometer-sized indentors. The results are described in terms of a rate-dependent and temperature-dependent phenomenological yield strength. We follow the structural change during indentation with a computer technique that allows us to model the dynamic simulation of diffraction patterns.
Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging.
Berndsen, Zachary T; Keller, Nicholas; Grimes, Shelley; Jardine, Paul J; Smith, Douglas E
2014-06-10
Many viruses use molecular motors that generate large forces to package DNA to near-crystalline densities inside preformed viral proheads. Besides being a key step in viral assembly, this process is of interest as a model for understanding the physics of charged polymers under tight 3D confinement. A large number of theoretical studies have modeled DNA packaging, and the nature of the molecular dynamics and the forces resisting the tight confinement is a subject of wide debate. Here, we directly measure the packaging of single DNA molecules in bacteriophage phi29 with optical tweezers. Using a new technique in which we stall the motor and restart it after increasing waiting periods, we show that the DNA undergoes nonequilibrium conformational dynamics during packaging. We show that the relaxation time of the confined DNA is >10 min, which is longer than the time to package the viral genome and 60,000 times longer than that of the unconfined DNA in solution. Thus, the confined DNA molecule becomes kinetically constrained on the timescale of packaging, exhibiting glassy dynamics, which slows the motor, causes significant heterogeneity in packaging rates of individual viruses, and explains the frequent pausing observed in DNA translocation. These results support several recent hypotheses proposed based on polymer dynamics simulations and show that packaging cannot be fully understood by quasistatic thermodynamic models.
Electronic excited states and relaxation dynamics in polymer heterojunction systems
Ramon, John Glenn Santos
The potential for using conducting polymers as the active material in optoelectronic devices has come to fruition in the past few years. Understanding the fundamental photophysics behind their operations points to the significant role played by the polymer interface in their performance. Current device architectures involve the use of bulk heterojunctions which intimately blend the donor and acceptor polymers to significantly increase not only their interfacial surface area but also the probability of exciton formation within the vicinity of the interface. In this dissertation, we detail the role played by the interface on the behavior and performance of bulk heterojunction systems. First, we explore the relation between the exciton binding energy to the band offset in determining device characteristics. As a general rule, when the exciton binding energy is greater than the band offset, the exciton remains the lowest energy excited state leading to efficient light-emitting properties. On the other hand, if the offset is greater than the binding energy, charge separation becomes favorable leading to better photovoltaic behavior. Here, we use a Wannier function, configuration interaction based approach to examine the essential excited states and predict the vibronic absorption and emission spectra of the PPV/BBL, TFB/F8BT and PFB/F8BT heterojunctions. Our results underscore the role of vibrational relaxation in the formation of charge-transfer states following photoexcitation. In addition, we look at the relaxation dynamics that occur upon photoexcitation. For this, we adopt the Marcus-Hush semiclassical method to account for lattice reorganization in the calculation of the interconversion rates in TFB/F8BT and PFB/F8BT. We find that, while a tightly bound charge-transfer state (exciplex) remains the lowest excited state, a regeneration pathway to the optically active lowest excitonic state in TFB/F8BT is possible via thermal repopulation from the exciplex. Finally
Dynamic Nuclear Polarization and Relaxation of H and D Atoms in Solid Mixtures of Hydrogen Isotopes
Sheludiakov, S.; Ahokas, J.; Järvinen, J.; Vainio, O.; Lehtonen, L.; Vasiliev, S.; Lee, D. M.; Khmelenko, V. V.
2016-12-01
We report on a study of dynamic nuclear polarization and electron and nuclear spin relaxation of atomic hydrogen and deuterium in solid molecular matrices of H2, D2 , and HD mixtures. The electron and nuclear spin relaxation times (T_{1e} and T_{1N} ) were measured within the temperature range 0.15-2.5 K in a magnetic field of 4.6 T, conditions which ensure a high polarization of electron spins. We found that T_{1e} is nearly temperature independent in this temperature range, while T_{1N} decreased by two orders of magnitude upon raising temperature. Such strong temperature dependence is typical for the nuclear Orbach mechanism of relaxation via the electron spins. We found that the nuclear spins of H atoms in solid D2 and D2{:}HD can be efficiently polarized by the Overhauser effect. Pumping the forbidden transitions of H atoms also leads to DNP, with the efficiency strongly dependent on the concentration of D atoms. This behavior indicates the cross effect mechanism of the DNP and nuclear relaxation, which turns out to be well resolved in the conditions of our experiments. Efficient DNP of H atoms was also observed when pumping the middle D line located in the center of the ESR spectrum. This phenomenon can be explained in terms of clusters or pairs of H atoms with a strong exchange interaction. These clusters have partially allowed transitions in the center of the ESR spectrum, and DNP may be created via the resolved cross effect.
Molecular motions in thermotropic liquid crystals studied by NMR spin-lattice relaxation
Zamar, R.C.; Gonzalez, C.E.; Mensio, O. [Cordoba Univ. Nacional (Argentina). Facultad de Matematica, Astronomia y Fisica
1998-12-01
Nuclear magnetic resonance relaxation experiments with field cycling techniques proved to be a valuable tool for studying molecular motions in liquid crystals, allowing a very broad Larmor frequency variation, sufficient to separate the cooperative motions from the liquid like molecular diffusion. In new experiments combining NMR field cycling with the Jeener-Broekaert order-transfer pulse sequence, it is possible to measure the dipolar order relaxation time (T{sub 1D}), in addition to the conventional Zeeman relaxation time (T{sub 1Z}) in a frequency range of several decades. When applying this technique to nematic thermotropic liquid crystals, T{sub 1D} showed to depend almost exclusively on the order fluctuation of the director mechanism in the whole frequency range. This unique characteristic of T{sub 1D} makes dipolar order relaxation experiments specially useful for studying the frequency and temperature dependence of the spectral properties of the collective motions. (author)
Uncovering Molecular Relaxation Processes with Nonlinear Spectroscopies in the Deep UV
West, Brantley Andrew
Conical intersections mediate internal conversion dynamics that compete with even the fastest nuclear motions in molecular systems. Traditional kinetic models do not apply in this regime of commensurate electronic and nuclear motion because the surroundings do not maintain equilibrium throughout the relaxation process. This dissertation focuses on uncovering the physics associated with vibronic interactions at conical intersections. Of particular interest are coherent nuclear motions driven by steep excited state potential energy gradients. Technical advances have only recently made these dynamics accessible in many systems including DNA nucleobases and cyclic polyene molecules. Optical analogues of multidimensional NMR spectroscopies have recently yielded transformative insight in relaxation processes ranging from energy transfer in photosynthesis to bond making and breaking in liquids. Prior to the start of this research, such experiments had only been conducted at infrared and visible wavelengths. Applications in the ultraviolet were motivated by studies of numerous biological systems (e.g., DNA, proteins), but had been challenged by technical issues. The work presented in this dissertation combines pulse generation techniques developed in the optical physics community with spectroscopic techniques largely pioneered by physical chemists to implement two-dimensional ultraviolet spectroscopy (2DUV). This technique is applied at the shortest wavelengths and with the best signal-to-noise ratios reported to date. Sub-picosecond excited state deactivation processes provide photo stability to the DNA double helix. Vibrational energy transfer from the solute to surrounding solvent enables relaxation of the highly non-equilibrium ground state produced by fast internal conversion. In this dissertation, nonlinear spectroscopies carried out at cryogenic temperatures are used to uncover the particular nuclear modes in the solvent that primarily accept vibrational energy from
Modified relaxation dynamics and coherent energy exchange in coupled vibration-cavity polaritons
Dunkelberger, A. D.; Spann, B. T.; Fears, K. P.; Simpkins, B. S.; Owrutsky, J. C.
2016-11-01
Coupling vibrational transitions to resonant optical modes creates vibrational polaritons shifted from the uncoupled molecular resonances and provides a convenient way to modify the energetics of molecular vibrations. This approach is a viable method to explore controlling chemical reactivity. In this work, we report pump-probe infrared spectroscopy of the cavity-coupled C-O stretching band of W(CO)6 and the direct measurement of the lifetime of a vibration-cavity polariton. The upper polariton relaxes 10 times more quickly than the uncoupled vibrational mode. Tuning the polariton energy changes the polariton transient spectra and relaxation times. We also observe quantum beats, so-called vacuum Rabi oscillations, between the upper and lower vibration-cavity polaritons. In addition to establishing that coupling to an optical cavity modifies the energy-transfer dynamics of the coupled molecules, this work points out the possibility of systematic and predictive modification of the excited-state kinetics of vibration-cavity polariton systems.
Molecular modelling and molecular dynamics of CFTR.
Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul
2017-01-01
The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.
Spin-lattice relaxation study of the methyl proton dynamics in solid 9,10-dimethyltriptycene (DMT).
Piślewski, N; Tritt-Goc, J; Bielejewski, M; Rachocki, A; Ratajczyk, T; Szymański, S
2009-06-01
Proton spin-lattice relaxation studies are performed for powder samples of 9,10-dimethyltriptycene (DMT) and its isotopomer DMT-d(12) in which all the non-methyl protons in the molecule are replaced by deuterons. The relaxation data are interpreted in terms of the conventional relaxation theory based on the random jump model in which the Pauli correlations between the relevant spin and torsional states are discarded. The Arrhenius activation energies, obtained from the relaxation data, 25.3 and 24.8 kJ mol(-1) for DMT and DMT-d(12), respectively, are very high as for the methyl groups. The validity of the jump model in the present case is considered from the perspective of Haupt theory in which the Pauli principle is explicitly invoked. To this purpose, the dynamic quantities entering the Haupt model are reinterpreted in the spirit of the damped quantum rotation (DQR) approach introduced recently for the purpose of NMR lineshape studies of hindered molecular rotators. Theoretical modelling of the relevant methyl group dynamics, based on the DQR theory, was performed. From these calculations it is inferred that direct assessments of the torsional barrier heights, based on the Arrhenius activation energies extracted from relaxation data, should be treated with caution.
Molecular crowding and protein enzymatic dynamics.
Echeverria, Carlos; Kapral, Raymond
2012-05-21
The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding.
Du, Jianqing; Zheng, Bo; Wang, Jian-Sheng
2006-05-01
Using a nonequilibrium relaxation method, we calculate the dynamic critical exponent z of the two-dimensional Ising model for the Swendsen-Wang and Wolff algorithms. We examine dynamic relaxation processes following a quench from a disordered or an ordered initial state to the critical temperature Tc, and measure the exponential relaxation time of the system energy. For the Swendsen-Wang algorithm with an ordered or a disordered initial state, and for the Wolff algorithm with an ordered initial state, the exponential relaxation time fits well to a logarithmic size dependence up to a lattice size L = 8192. For the Wolff algorithm with a disordered initial state, we obtain an effective dynamic exponent zexp = 1.19(2) up to L = 2048. For comparison, we also compute the effective dynamic exponents through the integrated correlation times. In addition, an exact result of the Swendsen-Wang dynamic spectrum of a one-dimensional Ising chain is derived.
Chua, Y. Z.; Young-Gonzales, A. R.; Richert, R.; Ediger, M. D.; Schick, C.
2017-07-01
Physical vapor deposition has been used to prepare glasses of ethanol. Upon heating, the glasses transformed into the supercooled liquid phase and then crystallized into the plastic crystal phase. The dynamic glass transition of the supercooled liquid is successfully measured by AC nanocalorimetry, and preliminary results for the plastic crystal are obtained. The frequency dependences of these dynamic glass transitions observed by AC nanocalorimetry are in disagreement with conclusions from previously published dielectric spectra of ethanol. Existing dielectric loss spectra have been carefully re-evaluated considering a Debye peak, which is a typical feature in the dielectric loss spectra of monohydroxy alcohols. The re-evaluated dielectric fits reveal a prominent dielectric Debye peak, a smaller and asymmetrically broadened peak, which is identified as the signature of the structural α-relaxation and a Johari-Goldstein secondary relaxation process. This new assignment of the dielectric processes is supported by the observation that the AC nanocalorimetry dynamic glass transition temperature, Tα, coincides with the dielectric structural α-relaxation process rather than the Debye process. The combined results from dielectric spectroscopy and AC nanocalorimetry on the plastic crystal of ethanol suggest the occurrence of a Debye process also in the plastic crystal phase.
Conformation and intramolecular relaxation dynamics of semiflexible randomly hyperbranched polymers
Kumar, Amit; Rai, Gobind Ji; Biswas, Parbati
2013-03-01
The conformational and dynamic properties of semiflexible randomly hyperbranched polymers are investigated in dilute solutions within the framework of optimized Rouse-Zimm formalism. Semiflexibility is incorporated by restricting the directions and orientations of the respective bond vectors, while hydrodynamic interactions are modeled through the preaveraged Oseen tensor. The effect of semiflexibility is typically reflected in the intermediate frequency regime of the viscoelastic relaxation moduli where the bond orientation angle restores the characteristic power-law scaling in fractal structures, as in randomly hyperbranched polymers. Despite the absence of this power-law scaling regime in flexible randomly hyperbranched polymers and in earlier models of semiflexible randomly branched polymers due to weak disorder [C. von Ferber and A. Blumen, J. Chem. Phys. 116, 8616 (2002)], 10.1063/1.1470198, this power-law behavior may be reinstated by explicitly modeling hyperbranched polymers as a Vicsek fractals. The length of this power-law zone in the intermediate frequency region is a combined function of the number of monomers and the degree of semiflexibility. A clear conformational transition from compact to open structures is facilitated by changing the bond orientation angle, where the compressed conformations are compact, while the expanded ones are relatively non-compact. The extent of compactness in the compressed conformations are much less compared to the semiflexible dendrimers, which resemble hard spheres. The fractal dimensions of the compressed and expanded conformations calculated from the Porod's scaling law vary as a function of the bond orientation angle, spanning the entire range of three distinct scaling regimes of linear polymers in three-dimensions. The results confirm that semiflexibility exactly accounts for the excluded volume interactions which are expected to be significant for such polymers with complex topologies.
Multiscale Reactive Molecular Dynamics
2012-08-15
as a linear combination of several possible bond- ing topologies ( diabatic states) that are coupled to one an- other through the off-diagonal elements...adapts and dynamically identifies bonding topolo- gies to include as the simulation progresses. These bonding topologies form a basis of diabatic ...the original geometric factor. The diabatic correction term, VCORR , used here was labeled in previous MS-EVB models as a repulsive interaction, VREP
State-Dependent Molecular Dynamics
Ciann-Dong Yang
2014-10-01
Full Text Available This paper proposes a new mixed quantum mechanics (QM—molecular mechanics (MM approach, where MM is replaced by quantum Hamilton mechanics (QHM, which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics.
Molecular dynamics simulation of the viscocapillary leveling of polymer films
Tanis, Ioannis; Salez, Thomas; Raphaël, Elie; Maggs, Anthony C; Baschnagel, Jörg
2016-01-01
Surface tension-driven flow techniques have recently emerged as an efficient means of shedding light into the rheology of thin polymer films. Motivated by experimental and theoretical approaches in films bearing a varying surface topography, we present results on the viscocapillary relaxation of a square pattern at the free surface of a polymer film, using molecular dynamics simulations of a coarse-grained polymer model. Height profiles are monitored as a function of time after heating the system above its glass-transition temperature. The associated relaxation rates are in agreement with the low-Reynolds-number hydrodynamic model, thus confirming the utility of the simulation method.
Molecular dynamics simulation of pyridine
Trumpakaj, Zygmunt; Linde, Bogumił
2015-04-01
Molecular Dynamics (MD) simulations are used for the investigation of molecular motions in pyridine in the temperature range 20-480 K under normal pressure. The results obtained are analyzed within the frame of the Mori Zwanzig memory function formalism. An analytical approximation of the first memory function K(t) is applied to predict some dependences on temperature. Experimental results of the Rayleigh scattering of depolarized light from liquid pyridine are used as the main base for the comparison.
Space and time dynamical heterogeneity in glassy relaxation. The role of democratic clusters
Appignanesi, G A; Rodriguez Fris, J A [Fisicoquimica, Departamento de Quimica, Universidad Nacional del Sur, Avenida Alem 1253, 8000 BahIa Blanca (Argentina); Seccion de Fisicoquimica, Instituto de Quimica de la Universidad Nacional del Sur, INQUISUR-UNS-CONICET, Universidad Nacional del Sur, Avenida Alem 1253, 8000 BahIa Blanca (Argentina)], E-mail: appignan@criba.edu.ar
2009-05-20
In this work we review recent computational advances in the understanding of the relaxation dynamics of supercooled glass-forming liquids. In such a supercooled regime these systems experience a striking dynamical slowing down which can be rationalized in terms of the picture of dynamical heterogeneities, wherein the dynamics can vary by orders of magnitude from one region of the sample to another and where the sizes and timescales of such slowly relaxing regions are expected to increase considerably as the temperature is decreased. We shall focus on the relaxation events at a microscopic level and describe the finding of the collective motions of particles responsible for the dynamical heterogeneities. In so doing, we shall demonstrate that the dynamics in different regions of the system is not only heterogeneous in space but also in time. In particular, we shall be interested in the events relevant to the long-time structural relaxation or {alpha} relaxation. In this regard, we shall focus on the discovery of cooperatively relaxing units involving the collective motion of relatively compact clusters of particles, called 'democratic clusters' or d-clusters. These events have been shown to trigger transitions between metabasins of the potential energy landscape (collections of similar configurations or structures) and to consist of the main steps in the {alpha} relaxation. Such events emerge in systems quite different in nature such as simple model glass formers and supercooled amorphous water. Additionally, another relevant issue in this context consists in the determination of a link between structure and dynamics. In this context, we describe the relationship between the d-cluster events and the constraints that the local structure poses on the relaxation dynamics, thus revealing their role in reformulating structural constraints. (topical review)
Coupling of caged molecule dynamics to Johari-Goldstein β-relaxation in metallic glasses
Wang, Z.; Ngai, K. L.; Wang, W. H.; Capaccioli, S.
2016-01-01
Three recently published papers have discovered a general property of the fast caged dynamics observed in the glassy states of polyalcohols (S. Capaccioli et al., J. Phys. Chem. B 119, 8800 (2015)), amorphous polymers (K. L. Ngai et al., J. Phys. Chem. B 119, 12502 (2015)), and van der Waals molecular glass-formers (K. L. Ngai et al., J. Phys. Chem. B 119, 12519 (2015)). The fast caged dynamics are manifested as nearly constant loss (NCL) in dielectric and mechanical susceptibility. Shown before in these papers is the intensity of the caged dynamics change temperature dependence at a temperature THF nearly coincident with the secondary glass transition temperature Tgβ, at which the Johari-Goldstein (JG) β-relaxation time τJG reaches ˜103 s. Evidently this finding indicates the coupling of the caged dynamics to the secondary glass transition. The glass-formers considered so far are all soft matters. However, the generality of the phenomenon and its explanation implies that the relation, THF ≈ Tgβ, should be observed in other classes of glass-formers. In this paper, we extend the consideration of the phenomenon and explanation to metallic glasses, which are not soft matter. The experimental data presented show the same phenomenon, supporting its generality and fundamental importance in the physics of glass and glass transition.
Dynamic molecular graphs: "hopping" structures.
Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María
2014-05-05
This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
A proton NMR relaxation study of water dynamics in bovine serum albumin nanoparticles.
Belotti, Monica; Martinelli, Andrea; Gianferri, Raffaella; Brosio, Elvino
2010-01-14
Water dynamics and compartmentation in glutaraldehyde cross-linked bovine serum albumin nanoparticles have been investigated by an integrated nuclear magnetic resonance (NMR) protocol based on water relaxation times and self-diffusion coefficients measurements. Multi-exponentially of water relaxation curves has been accounted for according to a diffusive and chemical exchange model (see B. P. Hills, S. F. Takacs and P. S. Belton, Mol. Phys., 1989, 67(4), 903, and Mol. Phys., 1989, 67(4), 913; E. Brosio, M. Belotti and R. Gianferri, in Food Science and Technology: New Research, ed. L. V. Greco and M. N. Bruno, Nova Science Publishers, Hauppauge (NY), 2008) that made it possible to single out water molecules in the molecular spaces in the interior of albumin nanoparticles, in the meso-cavities formed by packed nanoparticles and in the meniscus on top of the nanoparticles suspension. A quantitative rationalization of T(2) values of water different components allowed morphological information to be acquired as for the size of water filled compartments, while self-diffusion coefficient measurements of water excess or fluxed packed nanoparticles suspensions are describers of transport properties of soft biomaterials. The paper reports an NMR approach that can be seen as a general and relevant method to characterize excess-water-swollen soft biomaterials.
Molecular dynamics simulation of diffusivity
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Optical dynamics of molecular aggregates
de Boer, Steven
2006-01-01
The subject of this thesis is the spectroscopy and dynamics of molecular aggregates in amorphous matrices. Aggregates of three different molecules were studied. The molecules are depicted in Fig. (1.1). Supersaturated solutions of these molecules show aggregate formation. Aggregation is a process si
Coarse-grained protein molecular dynamics simulations
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Kinetic theories for spin models for cooperative relaxation dynamics
Pitts, Steven Jerome
The facilitated kinetic Ising models with asymmetric spin flip constraints introduced by Jackle and co-workers [J. Jackle, S. Eisinger, Z. Phys. B 84, 115 (1991); J. Reiter, F. Mauch, J. Jackle, Physica A 184, 458 (1992)] exhibit complex relaxation behavior in their associated spin density time correlation functions. This includes the growth of relaxation times over many orders of magnitude when the thermodynamic control parameter is varied, and, in some cases, ergodic-nonergodic transitions. Relaxation equations for the time dependence of the spin density autocorrelation function for a set of these models are developed that relate this autocorrelation function to the irreducible memory function of Kawasaki [K. Kawasaki, Physica A 215, 61 (1995)] using a novel diagrammatic series approach. It is shown that the irreducible memory function in a theory of the relaxation of an autocorrelation function in a Markov model with detailed balance plays the same role as the part of the memory function approximated by a polynomial function of the autocorrelation function with positive coefficients in schematic simple mode coupling theories for supercooled liquids [W. Gotze, in Liquids, Freezing and the Glass Transition, D. Levesque, J. P. Hansen, J. Zinn-Justin eds., 287 (North Holland, New York, 1991)]. Sets of diagrams in the series for the irreducible memory function are summed which lead to approximations of this type. The behavior of these approximations is compared with known results from previous analytical calculations and from numerical simulations. For the simplest one dimensional model, relaxation equations that are closely related to schematic extended mode coupling theories [W. Gotze, ibid] are also derived using the diagrammatic series. Comparison of the results of these approximate theories with simulation data shows that these theories improve significantly on the results of the theories of the simple schematic mode coupling theory type. The potential
Mechanical characterization of nanoindented graphene via molecular dynamics simulations
Wang Tong
2011-01-01
Full Text Available Abstract The mechanical behavior of graphene under various indentation depths, velocities, and temperatures is studied using molecular dynamics analysis. The results show that the load, elastic and plastic energies, and relaxation force increased with increasing indentation depth and velocity. Nanoindentation induced pile ups and corrugations of the graphene. Resistance to deformation decreased at higher temperature. Strong adhesion caused topological defects and vacancies during the unloading process.
王卫东; 郝跃; 纪翔; 易成龙; 牛翔宇
2012-01-01
分别采用Tersoff-Brenner势和AIREBO势，对三种长宽比的单层石墨烯纳米带在不同热力学温度（0．01—4000K）下的弛豫性能进行了分子动力学模拟．对基于两种势函数模拟的石墨烯纳米带弛豫的能量曲线和表面形貌进行了分析对比，研究了石墨烯纳米带在弛豫过程中的动态平衡过程．模拟结果表明：单层石墨烯纳米带并非完美的平面结构，边缘处和内部都会呈现一定程度的起伏和皱褶，这与已有的实验结果相符合；石墨烯纳米带的表面起伏程度随长宽比的减小而减小，并且在不同温度条件下，系统动能对石墨烯纳米带的弛豫变形的影响很大，即系统温度越高，石墨烯纳米带的弛豫变形幅度愈大；高长宽比纳米带在一定温度条件下甚至会出现卷曲现象．最后，对采用Tersoff-Brenner势和AIREBO势进行石墨烯的分子动力学模拟进行了深入分析．%At different thermodynamic temperatures (between 0.01 and 4000 K), the relaxation properties of three kinds of graphene nanorib- bons with different aspect ratios are simulated by molecular dynamics method based on Tersoff-Brenner and AIREBO potential func- tions separately. Then we compare the energy curves and surface morphologies of nanoribbon relaxation with two kinds of potential functions, and study the dynamic equilibrium process of the graphene nanoribbons during their relaxation simulation. The simulation results show that the single layer graphene nanoribbon is not of a perfect planar structure and that a certain degree of fluctuations and folds occur at the edges and inside of nanoribbons, which are consistent with the existing experimental results; the surface fluctuation level of graphene nanoribbons decreases with the reduction of the aspect ratio, and the system kinetic energy has a dramatic influence on the relaxation deformation of the graphene nanoribbons at different temperatures, which
Lajevardipour, Alireza; Chon, James W. M.; Chattopadhyay, Amitabha; Clayton, Andrew H. A.
2016-11-01
Spectral relaxation from fluorescent probes is a useful technique for determining the dynamics of condensed phases. To this end, we have developed a method based on wide-field spectral fluorescence lifetime imaging microscopy to extract spectral relaxation correlation times of fluorescent probes in living cells. We show that measurement of the phase and modulation of fluorescence from two wavelengths permit the identification and determination of excited state lifetimes and spectral relaxation correlation times at a single modulation frequency. For NBD fluorescence in glycerol/water mixtures, the spectral relaxation correlation time determined by our approach exhibited good agreement with published dielectric relaxation measurements. We applied this method to determine the spectral relaxation dynamics in membranes of living cells. Measurements of the Golgi-specific C6-NBD-ceramide probe in living HeLa cells revealed sub-nanosecond spectral dynamics in the intracellular Golgi membrane and slower nanosecond spectral dynamics in the extracellular plasma membrane. We interpret the distinct spectral dynamics as a result of structural plasticity of the Golgi membrane relative to more rigid plasma membranes. To the best of our knowledge, these results constitute one of the first measurements of Golgi rotational dynamics.
Lajevardipour, Alireza; Chon, James W M; Chattopadhyay, Amitabha; Clayton, Andrew H A
2016-11-22
Spectral relaxation from fluorescent probes is a useful technique for determining the dynamics of condensed phases. To this end, we have developed a method based on wide-field spectral fluorescence lifetime imaging microscopy to extract spectral relaxation correlation times of fluorescent probes in living cells. We show that measurement of the phase and modulation of fluorescence from two wavelengths permit the identification and determination of excited state lifetimes and spectral relaxation correlation times at a single modulation frequency. For NBD fluorescence in glycerol/water mixtures, the spectral relaxation correlation time determined by our approach exhibited good agreement with published dielectric relaxation measurements. We applied this method to determine the spectral relaxation dynamics in membranes of living cells. Measurements of the Golgi-specific C6-NBD-ceramide probe in living HeLa cells revealed sub-nanosecond spectral dynamics in the intracellular Golgi membrane and slower nanosecond spectral dynamics in the extracellular plasma membrane. We interpret the distinct spectral dynamics as a result of structural plasticity of the Golgi membrane relative to more rigid plasma membranes. To the best of our knowledge, these results constitute one of the first measurements of Golgi rotational dynamics.
Shiba, Hayato; Yamada, Yasunori; Kawasaki, Takeshi; Kim, Kang
2016-12-01
By using large-scale molecular dynamics simulations, the dynamics of two-dimensional (2D) supercooled liquids turns out to be dependent on the system size, while the size dependence is not pronounced in three-dimensional (3D) systems. It is demonstrated that the strong system-size effect in 2D amorphous systems originates from the enhanced fluctuations at long wavelengths which are similar to those of 2D crystal phonons. This observation is further supported by the frequency dependence of the vibrational density of states, consisting of the Debye approximation in the low-wave-number limit. However, the system-size effect in the intermediate scattering function becomes negligible when the length scale is larger than the vibrational amplitude. This suggests that the finite-size effect in a 2D system is transient and also that the structural relaxation itself is not fundamentally different from that in a 3D system. In fact, the dynamic correlation lengths estimated from the bond-breakage function, which do not suffer from those enhanced fluctuations, are not size dependent in either 2D or 3D systems.
Influence of hydroxypropyl cellulose on molecular relaxations of epoxy-amine networks
Maria Inez G. Miranda
2013-01-01
Full Text Available A dynamic mechanical analysis (DMTA study was conducted on epoxy-amine networks crosslinked in the presence of low contents of hydroxypropyl cellulose (HPC. The epoxy resin chosen was diglycidylether of bisphenol-A (DGEBA and the crosslinker was 4,4'-diaminodiphenylmethane (DDM. In the glassy region, primary (α and secondary (β, γ relaxations originating from the epoxy and HPC components were well detected. Two primary relaxations of neat epoxy and epoxy/HPC systems, referred to as αepoxy and α'epoxy, could be detected, showing a particular glassy behavior for the systems studied in comparison with systems cured in bulk. The main relaxation temperature Tα (at the peak of αepoxy relaxation of the epoxy systems increased slightly with the addition of HPC. The activation energy for this transition (Tα of the epoxy-amine networks was determined both from tan δ and the peak temperatures for the loss modulus measured at various frequencies. The activation energy of the αepoxy relaxation determined from the loss modulus was more reliable than that based on tan δ. The addition of HPC lowered the activation energy of this αepoxy relaxation.
Femtosecond Excited State Dynamics of Size Selected Neutral Molecular Clusters.
Montero, Raúl; León, Iker; Fernández, José A; Longarte, Asier
2016-07-21
The work describes a novel experimental approach to track the relaxation dynamics of an electronically excited distribution of neutral molecular clusters formed in a supersonic expansion, by pump-probe femtosecond ionization. The introduced method overcomes fragmentation issues and makes possible to retrieve the dynamical signature of a particular cluster from each mass channel, by associating it to an IR transition of the targeted structure. We have applied the technique to study the nonadiabatic relaxation of pyrrole homoclusters. The results obtained exciting at 243 nm, near the origin of the bare pyrrole electronic absorption, allow us to identify the dynamical signature of the dimer (Py)2, which exhibits a distinctive lifetime of τ1 ∼ 270 fs, considerably longer than the decays recorded for the monomer and bigger size clusters (Py)n>2. A possible relationship between the measured lifetime and the clusters geometries is tentatively discussed.
Nano-tribology through molecular dynamics simulations
WANG; Hui(
2001-01-01
［1］Burkert, U., Allinger, N. L., Molecular Mechanics, York: Maple Press Company, 1982.［2］Daw, M. S. , Baskes, M. I., Embedded-atom method: derivation and application to impurities, surface and other defects in metals, Phys. Rev. B, 1984, 29: 6443-6453.［3］Frenke, D., Smit, B., Understanding Molecular Simulation, San Diego: Academic Press, 1996, 60-67, 125-140.［4］Granick, S., Motions and relaxation of confined liquids, Science, 1991, 253: 1374-1379.［5］Koplik, J., Banavar, J., Willemsen, J., Molecular dynamics of Poisewulle flow and moving contact line, Phys. Rev.Lett., 1988, 60: 1282-1285.［6］Hu, Y. Z., Wang, H., Guo, Y. et al., Simulation of lubricant rheology in thin film lubrication, Part I: simulation of Poiseuille flow, Wear, 1996, 196: 243-259.［7］Zou, K., Li, Z. J, Leng, Y. S. et al. , Surface force apparatus and its application in the study of solid contacts, Chinese Science Bulletin, 1999, 44: 268-271.［8］Stevens, M. , Mondello, M., Grest, G. et al. , Comparison of shear flow of hexadecane in a confined geometry and in bulk,J. Chem. Phys., 1997, 106: 7303-7314.［9］Huang, P., Luo, J. B., Wen, S. Z., Theoretical study on the lubrication failure for tthe lubricants with a limiting shear stress, Tribology International, 1999, 32: 421-426.［10］Ryckaert, J. P. , Bellemans. , A molecular dynamics of alkanes, Faraday Soc. , 1978, 66: 95-106.［11］Wang, H. , Hu, Y. Z., A molecular dynamics study on slip phenomenon at solid-liquid interface, in Proceedings of tthe First AICT, Beijing: Tsinghua University Press, 1998, 295-299.［12］Landman, U., Luedtke, W., Burnham, N. et al., Mechanisms and dynamics of adhesion, nanoindentation, and fracture, Science, 1990, 248: 454-461.［13］Leng, Y. S., Hu, Y. Z., Zheng, L. Q., Adhesive contact of flat-ended wedges: theory and computer experiments, Journal of Tribology, 1999, 121: 128-132.
Grand canonical Molecular Dynamics Simulations
Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K
2011-01-01
For simulation studies of (macro-) molecular liquids it would be of significant interest to be able to adjust/increase the level of resolution within one region of space, while allowing for the free exchange of molecules between (open) regions of different resolution/representation. In the present work we generalize the adaptive resolution idea in terms of a generalized Grand Canonical approach. This provides a robust framework for truly open Molecular Dynamics systems. We apply the method to liquid water at ambient conditions.
Aso, Y; Yoshioka, S; Kojima, S
2000-03-01
Isothermal crystallization of amorphous nifedipine, phenobarbital, and flopropione was studied at temperatures above and below their glass transition temperatures (T(g)). A sharp decrease in the crystallization rate with decreasing temperature was observed for phenobarbital and flopropione, such that no crystallization was observed at temperatures 20-30 degrees C lower than their T(g) within ordinary experimental time periods. In contrast, the crystallization rate of nifedipine decreased moderately with decreasing temperature, and considerable crystallization was observed at 40 degrees C below its T(g) within 4 months. The molecular mobility of these amorphous drugs was assessed by enthalpy relaxation and (1)H-NMR relaxation measurements. The enthalpy relaxation time of nifedipine was smaller than that of phenobarbital or flopropinone at the same T - T(g) values, suggesting higher molecular mobility of nifedipine. The spin-lattice relaxation time in the rotating frame (T(1rho)) decreased markedly at temperature above T(g). The slope of the Arrhenius type plot of the T(1rho) for nifedipine protons changed at about 10 degrees C below the T(g), whereas the slope for phenobarbital protons became discontinuous at about 10 degrees C above the T(g). Even at temperatures below its T(g), the spin-spin relaxation process of nifedipine could be described by the sum of its Gaussian relaxation, which is characteristic of solid protons, and its Lorentzian relaxation, which is characteristic of protons with higher mobility. In contrast, no Lorentzian relaxation was observed for phenobarbital or flopropione at temperatures below their T(g). These results also suggest that nifedipine has higher molecular mobility than phenobarbital and flopropione at temperatures below T(g). The faster crystallization of nifedipine than that of phenobarbital or flopropione observed at temperatures below its T(g) may be partly ascribed to its higher molecular mobility at these temperatures.
Dielectric relaxation dynamics of high-temperature piezoelectric polyimide copolymers
Maceiras, A.; Costa, C. M.; Lopes, A. C.; San Sebastián, M.; Laza, J. M.; Vilas, J. L.; Ribelles, J. L. Gómez; Sabater i Serra, R.; Andrio Balado, A.; Lanceros-Méndez, S.; León, L. M.
2015-08-01
Polyimide copolymers have been prepared based on different diamines as comonomers: a diamine without CN groups and a novel synthesized diamine with two CN groups prepared by polycondensation reaction followed by thermal cyclodehydration. Dielectric spectroscopy measurements were performed, and the dielectric complex function, ac conductivity and electric modulus of the copolymers were investigated as a function of CN group content in the frequency range from 0.1 to 107 Hz at temperatures from 25 to 260 °C. For all samples and temperatures above 150 °C, the dielectric constant increases with increasing temperature due to increasing conductivity. The α-relaxation is just detected for the sample without CN groups, being this relaxation overlapped by the electrical conductivity contributions in the remaining samples. For the copolymer samples and the polymer with CN groups, an important Maxwell-Wagner-Sillars contribution is detected. The mechanisms responsible for the dielectric relaxation, conduction process and electric modulus response have been discussed as a function of the CN group content present in the samples.
From Molecular Dynamics to Brownian Dynamics
Erban, Radek
2014-01-01
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
Energy-resolved hot carrier relaxation dynamics in monocrystalline plasmonic nanoantennas
Méjard, Régis; Petit, Marlène; Bouhelier, Alexandre; Cluzel, Benoît; Demichel, Olivier
2016-01-01
Hot carriers are energetic photo-excited carriers driving a large range of chemico-physical mechanisms. At the nanoscale, an efficient generation of these carriers is facilitated by illuminating plasmonic antennas. However, the ultrafast relaxation rate severally impedes their deployment in future hot-carrier based devices. In this paper, we report on the picosecond relaxation dynamics of hot carriers in plasmonic monocrystalline gold nanoantennas. The temporal dynamics of the hot carriers is experimentally investigated by interrogating the nonlinear photoluminescence response of the antenna with a spectrally-resolved two-pulse correlation configuration. We measure time-dependent nonlinearity orders varying from 1 to 8, which challenge the common interpretation of multi-photon gold luminescence. We demonstrate that the relaxation of the photo-excited carriers depends of their energies relative to the Fermi level. We find a 60 % variation in the relaxation rate for electron-hole pair energies ranging from c.a....
Available Instruments for Analyzing Molecular Dynamics Trajectories.
Likhachev, I V; Balabaev, N K; Galzitskaya, O V
2016-01-01
Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed.
Wu, Xuebang; Guo, Lijun; Liu, C. S.
2014-06-01
The dynamics of the Johari-Goldstein (JG) β relaxation and the α relaxation in bulk metallic glasses (MGs) has been investigated by using mechanical spectroscopy combined with the Coupling Model. The β relaxations of MGs exhibit different behaviors such as peaks, humps, and excess wings due to the different fluctuations of the chemical interactions among the constituting atoms. A universal correlation between the β relaxation and the α relaxation is generally found by their activation energies and relaxation times as well as the non-exponentiality parameter of the α relaxation, which can be predicted quantitatively from the Coupling Model. Based on the quasi-point defects theory, a correlation factor χ shows a broad peak along with the β relaxation, suggesting that the concentration and the correlation degree of the string-like configurations involved in the β relaxation vary with increasing temperature, which challenges the previous view that the system is in an iso-configuration state below Tg and may shed new light on the nature of the JG β relaxation in metallic glasses.
Molecular Dynamics for Dense Matter
Maruyama, Toshiki; Chiba, Satoshi
2012-01-01
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions on the nuclear structure. First we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that the pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we dis...
Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)
2015-12-15
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.
Poveda, Ana [Universidad Autonoma de Madrid, Servicio Interdepartamental de Investigacion (Spain); Asensio, Juan Luis; Martin-Pastor, Manuel; Jimenez-Barbero, Jesus [Instituto de Quimica Organica, CSIC, Grupo de Carbohidratos (Spain)
1997-07-15
{sup 1}H-NMR cross-relaxation rates and nonselective longitudinal relaxation times have been obtained at two magnetic fields (7.0 and 11.8 T) and at a variety of temperatures for the branched tetrasaccharide methyl 3-O-{alpha}-N-acetyl-galactosaminyl-{beta}-galactopyranosyl-(1{sup {yields}}4)[3-O-{alpha}-fucosyl] -glucopyranoside (1), an inhibitor of astrocyte growth. In addition, {sup 13}C-NMR relaxation data have also been recorded at both fields. The {sup 1}H-NMR relaxation data have been interpreted using different motional models to obtain proton-proton correlation times. The results indicate that the GalNAc and Fuc rings display more extensive local motion than the two inner Glc and Gal moieties, since those present significantly shorter local correlation times. The{sup 13}C-NMR relaxation parameters have been interpreted in terms of the Lipari-Szabo model-free approach. Thus, order parameters and internal motion correlation times have been deduced. As obtained for the{sup 1}H-NMR relaxation data, the two outer residues possess smaller order parameters than the two inner rings. Internal correlation times are in the order of 100 ps. The hydroxymethyl groups have also different behaviour,with the exocyclic carbon on the glucopyranoside unit showing the highestS{sup 2}. Molecular dynamics simulations using a solvated system have also been performed and internal motion correlation functions have been deduced from these calculations. Order parameters and interproton distances have been compared to those inferred from the NMR measurements. The obtained results are in fair agreement with the experimental data.
Kurauskas, Vilius; Weber, Emmanuelle; Hessel, Audrey; Ayala, Isabel; Marion, Dominique; Schanda, Paul
2016-09-01
Transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance provide information about molecular motions occurring on nanosecond-to-millisecond (ns-ms) time scales. The measurement of heteronuclear ((13)C, (15)N) relaxation rate constants in the presence of a spin-lock radiofrequency field (R1ρ relaxation) provides access to such motions, and an increasing number of studies involving R1ρ relaxation in proteins have been reported. However, two factors that influence the observed relaxation rate constants have so far been neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR) and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that the CCR rate constant depends on ns-ms motions; it can thus provide insight into dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling effect on the doublet components. For measurements of dynamics, the use of R1ρ rate constants has practical advantages over the use of CCR rates, and this article reveals factors that have so far been disregarded and which are important for accurate measurements and interpretation.
Shete, Ganesh; Khomane, Kailas S; Bansal, Arvind Kumar
2014-01-01
The purpose of this paper was to investigate the relaxation behavior of amorphous hesperetin (HRN), using dielectric spectroscopy, and assessment of its crystallization kinetics above glass transition temperature (Tg ). Amorphous HRN exhibited both local (β-) and global (α-) relaxations. β-Relaxation was observed below Tg , whereas α-relaxation prominently emerged above Tg . β-Relaxation was found to be of Johari-Goldstein type and was correlated with α-process by coupling model. Secondly, isothermal crystallization experiments were performed at 363 K (Tg + 16.5 K), 373 K (Tg + 26.5 K), and 383 K (Tg + 36.5 K). The kinetics of crystallization, obtained from the normalized dielectric strength, was modeled using the Avrami model. Havriliak-Negami (HN) shape parameters, αHN and αHN .βHN , were analyzed during the course of crystallization to understand the dynamics of amorphous phase during the emergence of crystallites. HN shape parameters indicated that long range (α-like) were motions affected to a greater extent than short range (β-like) motions during isothermal crystallization studies at all temperature conditions. The variable behavior of α-like motions at different isothermal crystallization temperatures was attributed to evolving crystallites with time and increase in electrical conductivity with temperature.
Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-01-01
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and
Molecular Biodynamers : Dynamic Covalent Analogues of Biopolymers
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-01-01
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and
Scalable molecular dynamics with NAMD.
Phillips, James C; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D; Kalé, Laxmikant; Schulten, Klaus
2005-12-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. (c) 2005 Wiley Periodicals, Inc.
Rheology via nonequilibrium molecular dynamics
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference.
Wu Xuebang
2015-09-01
Full Text Available The general trend in soft matter is to study systems of increasing complexity covering a wide range in time and frequency. Mechanical spectroscopy is a powerful tool for understanding the structure and relaxation dynamics of these materials over a large temperature range and frequency scale. In this work, we collect a few recent applications using low-frequency mechanical spectroscopy for elucidating the structural changes and relaxation dynamics in soft matter, largely based on the author’s group. We illustrate the potential of mechanical spectroscopy with three kinds of soft materials: colloids, polymers and granular systems. Examples include structural changes in colloids, segmental relaxations in amorphous polymers, and resonant dissipation of grain chains in three-dimensional media. The present work shows that mechanical spectroscopy has been applied as a necessary and complementary tool to study the dynamics of such complex systems.
Collective relaxation dynamics and crystallization kinetics of the amorphous Biclotymol antiseptic.
Tripathi, Pragya; Romanini, Michela; Tamarit, Josep Lluis; Macovez, Roberto
2015-11-10
We employ dielectric spectroscopy to monitor the relaxation dynamics and crystallization kinetics of the Biclotymol antiseptic in its amorphous phase. The glass transition temperature of the material as determined by dielectric spectroscopy is Tg = 290 ± 1K. The primary (α) relaxation dynamics is observed to follow a Vogel-Fulcher-Tammann temperature dependence, with a kinetic fragility index m = 86 ± 13, which classifies Biclotymol as a relatively fragile glass former. A secondary relaxation is also observed, corresponding to an intramolecular dynamic process of the non-rigid Biclotymol molecule. The crystallization kinetics, measured at four different temperatures above the glass transition temperature, follows an Avrami behavior with exponent virtually equal to n = 2, indicating one-dimensional crystallization into needle-like crystallites, as experimentally observed, with a time-constant nucleation rate. The activation barrier for crystallization is found to be Ea = 115 ± 22 kJ mol(-1).
Osmosis : a molecular dynamics computer simulation study
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver
2015-06-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)
2015-06-28
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Lin, Yu; Tan, Yeqiang; Qiu, Biwei; Shangguan, Yonggang; Harkin-Jones, Eileen; Zheng, Qiang
2013-01-17
The influence of annealing above the glass transition temperature (T(g)) on chain entanglement and molecular dynamics of solution-cast poly(methyl methacrylate)/poly(styrene-co-maleic anhydride) (PMMA/SMA) blends was investigated via a combination of dynamic rheological measurement and broadband dielectric spectroscopy. Chain entanglement density increases when the annealing temperature and/or time increases, resulting from the increased efficiency of chain packing and entanglement recovery. The results of the annealing treatment without cooling revealed that the increase of the entanglement density occurred during the annealing process instead of the subsequent cooling procedure. Annealing above T(g) exerts a profound effect on segmental motion, including the transition temperature and dynamics. Namely, T(g) shifts to higher temperatures and the relaxation time (τ(max)) increases due to the increased entanglement density and decreased molecular mobility. Either T(g) or τ(max) approaches an equilibrium value gradually, corresponding to the equilibrium entanglement density that might be obtained through the theoretical predictions. However, no obvious distribution broadening is observed due to the unchanged heterogeneous dynamics. Furthermore, side group rotational motion could be freely achieved without overcoming the chain entanglement resistance. Hence, neither the dynamics nor the distribution width of the subglass relaxation (β- and γ-relaxation) processes is affected by chain entanglement resulting from annealing, indicating that the local environment of the segments is unchanged.
Relaxation Dynamics of Ferroelectric Liquid Crystals in Pulsed Electric Field
Kudreyko, A. A.; Migranov, N. G.; Migranova, D. N.
2016-11-01
In this contribution we report a theoretical study of relaxation processes in surface-stabilized ferroelectric liquid crystals with spontaneous polarization. The influence of pulsed electric field on the behavior of ferroelectric liquid crystal in the SmC* phase, which is placed in a thin cell with strong anchoring of SmC* molecules with the boundary substrate, is studied. In the vicinity of the substrate interface, temporal dependence of the azimuthal motion of the director induced by electric field is obtained. The response to the external distortion of ferroelectric liquid crystal confined between two microstructured substrates is the occurrence of periodic temporal formation of solitons connected with the distortion of the director field n in the sample bulk. The interplay between microstructured substrates and director distribution of the ferroelectric SmC* phase is explained by the Frenkel-Kontorova model for a chain of atoms, but adapted for the continuum problem.
Electrical relaxation dynamics in TiO2 – polymer matrix composites
2007-12-01
Full Text Available Polymer matrix-TiO2 composites were prepared in three different filler concentrations. The electrical relaxation dynamics as well as the electrical conductivity of all samples were examined by means of Broadband Dielectric Spectroscopy (BDS over a wide frequency and temperature range. The recorded relaxation response includes contributions from both the polymer matrix and the reinforcing phase. Two relaxation modes (β and γ are observed in the low temperature region, which are attributed to the re-orientation of polar side groups of the matrix and rearrangement of small parts of the polymeric chain respectively. The α-relaxation and the Maxwell-Wagner-Sillars effect (MWS, attributed to the glassrubber transition of the polymeric matrix and to interfacial polarization phenomena respectively, are observed in the high temperature region. These two mechanisms are superimposed, thus a computer simulation procedure was followed in order to distinguish them. MWS effect becomes more pronounced with increasing concentration of the filler following an Arrhenius behaviour. The relaxation frequencies corresponding to α-mode follow the Vogel-Tamann-Fulcher (VTF equation. An additional relaxation mode is recorded at relatively high temperatures and high frequencies. Its occurrence and dynamics are related to the presence and the concentration of the filler. Finally, the Direct Current (DC conductivity follows the VTF equation.
Relaxation dynamics of a quantum emitter resonantly coupled to a metal nanoparticle
Nerkararyan, K. V.; Bozhevolnyi, S. I.
2014-01-01
The presence of a metal nanoparticle (MNP) near a quantum dipole emitter, when a localized surface plasmon mode is excited via the resonant coupling with an excited quantum dipole, dramatically changes the relaxation dynamics: an exponential decay changes to step-like behavior. The main physical...... consequence of this relaxation process is that the emission, being largely determined by the MNP, comes out with a substantial delay. A large number of system parameters in our analytical description opens new possibilities for controlling quantum emitter dynamics. (C) 2014 Optical Society of America...
Ultrafast Relaxation Dynamics of Photoexcited Zinc-Porphyrin: Electronic-Vibrational Coupling.
Abraham, Baxter; Nieto-Pescador, Jesus; Gundlach, Lars
2016-08-18
Cyclic tetrapyrroles are the active core of compounds with crucial roles in living systems, such as hemoglobin and chlorophyll, and in technology as photocatalysts and light absorbers for solar energy conversion. Zinc-tetraphenylporphyrin (Zn-TPP) is a prototypical cyclic tetrapyrrole that has been intensely studied in past decades. Because of its importance for photochemical processes the optical properties are of particular interest, and, accordingly, numerous studies have focused on light absorption and excited-state dynamics of Zn-TPP. Relaxation after photoexcitation in the Soret band involves internal conversion that is preceded by an ultrafast process. This relaxation process has been observed by several groups. Hitherto, it has not been established if it involves a higher lying "dark" state or vibrational relaxation in the excited S2 state. Here we combine high time resolution electronic and vibrational spectroscopy to show that this process constitutes vibrational relaxation in the anharmonic S2 potential.
Better, Cheaper, Faster Molecular Dynamics
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
Two-body relaxation in modified Newtonian dynamics
Ciotti, L
2004-01-01
A naive extension to MOND of the standard computation of the two-body relaxation time Tb implies that Tb is comparable to the crossing time regardless of the number N of stars in the system. This computation is questionable in view of the non-linearity of MOND's field equation. A non-standard approach to the calculation of Tb is developed that can be extended to MOND whenever discreteness noise generates force fluctuations that are small compared to the mean-field force. It is shown that this approach yields standard Newtonian results for systems in which the mean density profile is either plane-parallel or spherical. In the plane-parallel case we find that in the deep-MOND regime Tbb scales with N as in the Newtonian case, but is shorter by the square of the factor by which MOND enhances the gravitational force over its Newtonian value for the same system. Application of these results to dwarf galaxies and groups and clusters of galaxies reveals that in MOND luminosity segregation should be far advanced in g...
Stellar Dynamics around a Massive Black Hole II: Resonant Relaxation
Sridhar, S
2015-01-01
We present a first-principles theory of Resonant Relaxation (RR) of stellar systems orbiting within the sphere of influence of massive black holes in galactic nuclei. We extend the rigorous kinetic theory of Gilbert (1968) to include the Keplerian field of a black hole of mass $M_\\bullet$, and specialize to a (Keplerian) stellar system of mass $M \\ll M_\\bullet$. Using the results of the secular collisionless theory of Paper I, we orbit-average the kinetic equation through perturbative development in the small parameter $\\varepsilon = M/M_\\bullet$. This is supplemented with contributions from general relativistic corrections up to 1.5 post-Newtonian order and external gravitational sources. The result is a kinetic equation for a secular distribution function (DF) in 5-dim (Gaussian Ring) space, with explicit forms for the fluctuation and dissipation components of the collision integral. For general DFs, both apsidal and nodal precessions contribute to RR; so the traditional, physically-motivated distinction be...
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Molecular dynamics of interface rupture
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Molecular Dynamics Simulations of Polyelectrolyte Solutions
Dobrynin, Andrey
2014-03-01
Polyelectrolytes are polymers with ionizable groups. In polar solvents, these groups dissociate releasing counterions into solution and leaving uncompensated charges on the polymer backbone. Examples of polyelectrolytes include biopolymers such as DNA and RNA, and synthetic polymers such as poly(styrene sulfonate) and poly(acrylic acids). In this talk I will discuss recent molecular dynamics simulations of static and dynamic properties of polyelectrolyte solutions. These simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I - 1 / 2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ~ I- 1 / 5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ~ I- 1 / 2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ~ cp-1 / 4 . While at high salt concentrations one observes a weaker dependence of the chain size on the solution ionic strength, R ~ I- 1 / 8. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X (I) in salt solutions and corresponding quantities X (I0) in salt-free solutions, X (I) = X (I0) (I /I0) β . The exponent β = -1/2 for chain persistence length lp , β = 1/4 for solution correlation length, β = -1/5 and β = -1/8 for chain size R in dilute and semidilute solution regimes respectively. Furthermore, the analysis of the spectrum and of the relaxation times of Rouse modes confirms existence of the single length scale (correlation length) that controls both static and dynamic properties of semidilute polyelectrolyte solutions. These findings
How Stokes Shift Relaxation Reports on Poincar\\'e Recurrences in Host Dynamics
Mazur, Alexey K
2016-01-01
Recently it has been revealed that the equilibrium hydrogen-bond breathing dynamics of terminal base pairs in short DNA exhibit a power-law relaxation similar to that in the time-resolved Stokes shift experiments with an intercalated coumarin probe. Here a simple theory is proposed that relates the Stokes shift signal to the statistics of Poincar\\'e recurrences in the base-pair breathing. This theory can explain the origin of the observed slow non-exponential relaxation in time-resolved Stokes shift data for DNA as well as other complex systems. It turns out that an intercalated coumarin greatly increases the breathing fluctuations in the neighboring base pairs. This motion is qualitatively similar to that in terminal residues, with the same exponent in the power-law relaxation decay. The breathing dynamics is transmitted to the photoprobe by direct contacts between aromatic $\\pi$ orbitals of stacked bases.
Viciosa, M Teresa; Moura Ramos, Joaquim J; Diogo, Hermínio P
2016-12-01
The slow molecular mobility in the amorphous solid state of 3 active pharmaceutical drugs (cimetidine, nizatidine, and famotidine) has been studied using differential scanning calorimetry and the 2 dielectric-related techniques of dielectric relaxation spectroscopy and thermally stimulated depolarization currents. The glass-forming ability, the glass stability, and the tendency for crystallization from the equilibrium melt were investigated by differential scanning calorimetry, which also provided the characterization of the main relaxation of the 3 glass formers. The chemical instability of famotidine at the melting temperature and above it prevented the preparation of the amorphous for dielectric studies. In contrast, for cimetidine and nizatidine, the dielectric study yielded the main kinetic features of the α relaxation and of the secondary relaxations. According to the obtained results, nizatidine displays the higher fragility index of the 3 studied glass-forming drugs. The thermally stimulated depolarization current technique has proved useful to identify the Johari-Goldstein relaxation and to measure τβJG in the amorphous solid state, that is, in a frequency range which is not easily accessible by dielectric relaxation spectroscopy. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.
Nelson, Tammie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Center for Nonlinear Studies (CNLS) and Center for Integrated Nanotechnologies (CINT), Theoretical Division; Fernandez-Alberti, Sebastian [Univ. Nacional de Quilmes, Buenos Aires (Argentina); Chernyak, Vladimir [Wayne State Univ., Detroit, MI (United States). Dept. of Chemistry; Roitberg, Adrian E. [Univ. of Florida, Gainesville, FL (United States). Depts. of Physics and Chemistry. Quantum Theory Project; Tretiak, Sergei [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Center for Nonlinear Studies (CNLS) and Center for Integrated Nanotechnologies (CINT), Theoretical Division
2011-01-10
Nonadiabatic dynamics generally defines the entire evolution of electronic excitations in optically active molecular materials. It is commonly associated with a number of fundamental and complex processes such as intraband relaxation, energy transfer, and light harvesting influenced by the spatial evolution of excitations and transformation of photoexcitation energy into electrical energy via charge separation (e.g., charge injection at interfaces). To treat ultrafast excited-state dynamics and exciton/charge transport we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework incorporating quantum transitions. Our calculations rely on the use of the Collective Electronic Oscillator (CEO) package accounting for many-body effects and actual potential energy surfaces of the excited states combined with Tully’s fewest switches algorithm for surface hopping for probing nonadiabatic processes. This method is applied to model the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene, PPV). Our analysis shows intricate details of photoinduced vibronic relaxation and identifies specific slow and fast nuclear motions that are strongly coupled to the electronic degrees of freedom, namely, torsion and bond length alternation, respectively. Nonadiabatic relaxation of the highly excited mA{sub g} state is predicted to occur on a femtosecond time scale at room temperature and on a picosecond time scale at low temperature.
Demontis, Pierfranco; Gulín-González, Jorge; Masia, Marco; Sant, Marco; Suffritti, Giuseppe B
2015-06-28
In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between "fragile" (at higher temperatures) and "strong" (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between "fragile" (at lower temperatures) and "strong" (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T(∗) ∼ 315 ± 5 K, was spotted at T(∗) ∼ 283 K and T(∗) ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two
Ice formation on kaolinite: Insights from molecular dynamics simulations
Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos
2016-12-01
The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.
Rotational relaxation in molecular hydrogen and deuterium: Theory versus acoustic experiments
Montero, S., E-mail: emsalvador@iem.cfmac.csic.es [Laboratory of Molecular Fluid Dynamics @ Instituto de Estructura de la Materia, CSIC, Serrano 121, 28006 Madrid (Spain); Pérez-Ríos, J. [Physics Department, Purdue University, West Lafayette, Indiana 47907 (United States)
2014-09-21
An explicit formulation of the rotational relaxation time in terms of state-to-state rate coefficients associated to inelastic collisions is reported. The state-to-state rates needed for the detailed interpretation of relaxation in H{sub 2} and D{sub 2}, including isotopic variant mixtures, have been calculated by solving the close-coupling Schrödinger equations using the H{sub 2}–H{sub 2} potential energy surface by Diep and Johnson [J. Chem. Phys. 112, 4465 (2000)]. Relaxation related quantities (rotational effective cross section, bulk viscosity, relaxation time, and collision number) calculated from first principles agree reasonably well with acoustic absorption experimental data on H{sub 2} and D{sub 2} between 30 and 293 K. This result confirms at once the proposed formulation, and the validation of the H{sub 2}–H{sub 2} potential energy surface employed, since no approximations have been introduced in the dynamics. Accordingly, the state-to-state rates derived from Diep and Johnson potential energy surface appear to be overestimated by up to 10% for H{sub 2}, and up to 30% for D{sub 2} at T = 300 K, showing a better agreement at lower temperatures.
Traaseth, Nathaniel J; Chao, Fa-An; Masterson, Larry R; Mangia, Silvia; Garwood, Michael; Michaeli, Shalom; Seelig, Burckhard; Veglia, Gianluigi
2012-06-01
NMR relaxation methods probe biomolecular motions over a wide range of timescales. In particular, the rotating frame spin-lock R(1ρ) and Carr-Purcell-Meiboom-Gill (CPMG) R(2) experiments are commonly used to characterize μs to ms dynamics, which play a critical role in enzyme folding and catalysis. In an effort to complement these approaches, we introduced the Heteronuclear Adiabatic Relaxation Dispersion (HARD) method, where dispersion in rotating frame relaxation rate constants (longitudinal R(1ρ) and transverse R(2ρ)) is created by modulating the shape and duration of adiabatic full passage (AFP) pulses. Previously, we showed the ability of the HARD method to detect chemical exchange dynamics in the fast exchange regime (k(ex)∼10(4)-10(5) s(-1)). In this article, we show the sensitivity of the HARD method to slower exchange processes by measuring R(1ρ) and R(2ρ) relaxation rates for two soluble proteins (ubiquitin and 10C RNA ligase). One advantage of the HARD method is its nominal dependence on the applied radio frequency field, which can be leveraged to modulate the dispersion in the relaxation rate constants. In addition, we also include product operator simulations to define the dynamic range of adiabatic R(1ρ) and R(2ρ) that is valid under all exchange regimes. We conclude from both experimental observations and simulations that this method is complementary to CPMG-based and rotating frame spin-lock R(1ρ) experiments to probe conformational exchange dynamics for biomolecules. Finally, this approach is germane to several NMR-active nuclei, where relaxation rates are frequency-offset independent. Copyright © 2012 Elsevier Inc. All rights reserved.
Multivariable dynamic ankle mechanical impedance with relaxed muscles.
Lee, Hyunglae; Krebs, Hermano Igo; Hogan, Neville
2014-11-01
Neurological or biomechanical disorders may distort ankle mechanical impedance and thereby impair locomotor function. This paper presents a quantitative characterization of multivariable ankle mechanical impedance of young healthy subjects when their muscles were relaxed, to serve as a baseline to compare with pathophysiological ankle properties of biomechanically and/or neurologically impaired patients. Measurements using a highly backdrivable wearable ankle robot combined with multi-input multi-output stochastic system identification methods enabled reliable characterization of ankle mechanical impedance in two degrees-of-freedom (DOFs) simultaneously, the sagittal and frontal planes. The characterization included important ankle properties unavailable from single DOF studies: coupling between DOFs and anisotropy as a function of frequency. Ankle impedance in joint coordinates showed responses largely consistent with a second-order system consisting of inertia, viscosity, and stiffness in both seated (knee flexed) and standing (knee straightened) postures. Stiffness in the sagittal plane was greater than in the frontal plane and furthermore, was greater when standing than when seated, most likely due to the stretch of bi-articular muscles (medial and lateral gastrocnemius). Very low off-diagonal partial coherences implied negligible coupling between dorsiflexion-plantarflexion and inversion-eversion. The directions of principal axes were tilted slightly counterclockwise from the original joint coordinates. The directional variation (anisotropy) of ankle impedance in the 2-D space formed by rotations in the sagittal and frontal planes exhibited a characteristic "peanut" shape, weak in inversion-eversion over a wide range of frequencies from the stiffness dominated region up to the inertia dominated region. Implications for the assessment of neurological and biomechanical impairments are discussed.
Relaxation dynamics in the columnar liquid crystal phase of hard platelets
patti, A; Belli, S; van Roij, R.H.H.G.; Dijkstra, M.
2011-01-01
We perform Monte Carlo simulations to analyze the equilibrium dynamics and the long-time structural relaxation decay of columnar liquid crystals of disk-like colloidal particles. In the wake of recent studies on the columnar mesophase of hard calamitic (rod-like) colloids, we now focus on the
Carrier relaxation dynamics in InAs/InGaAlAs quantum dashes
Ryasnyanskiy, A.I.
2011-03-01
We characterize size-dependent carrier relaxation dynamics of partial laser structures containing quantum dashes by time-resolved degenerate four wave mixing between 1.2 and 1.6 ?m. © 2010 Elsevier B.V. All rights reserved.
Relaxation dynamics of glasses along a wide stability and temperature range
Rodríguez-Tinoco, C.; Ràfols-Ribé, J.; González-Silveira, M.; Rodríguez-Viejo, J.
2016-10-01
While lots of measurements describe the relaxation dynamics of the liquid state, experimental data of the glass dynamics at high temperatures are much scarcer. We use ultrafast scanning calorimetry to expand the timescales of the glass to much shorter values than previously achieved. Our data show that the relaxation time of glasses follows a super-Arrhenius behaviour in the high-temperature regime above the conventional devitrification temperature heating at 10 K/min. The liquid and glass states can be described by a common VFT-like expression that solely depends on temperature and limiting fictive temperature. We apply this common description to nearly-isotropic glasses of indomethacin, toluene and to recent data on metallic glasses. We also show that the dynamics of indomethacin glasses obey density scaling laws originally derived for the liquid. This work provides a strong connection between the dynamics of the equilibrium supercooled liquid and non-equilibrium glassy states.
Wang, Zi; Bevan, Kirk H.
2016-01-01
In the present work, we study the effects of the electronic relaxation of semicore levels on polaron activation energies and dynamics. Within the framework of adiabatic ab initio theory, we utilize both static transition state theory and molecular dynamics methods for an in-depth study of polaronic hopping in delithiated LiFePO4 (FePO4). Our results show that electronic relaxation of semicore states is significant in FePO4, resulting in a lower activation barrier and kinetics that is one to two orders faster compared to the result of calculations that do not incorporate semicore states. In general, the results suggest that the relaxation of states far below the Fermi energy could dramatically impact the ab initio polaronic barrier estimates for many transition metal oxides and phosphates.
Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations
Paavilainen, S.; Rog, T.; Vattulainen, I.
2011-01-01
We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile, no sign......We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile......, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril....
Applications and Implications of Fractional Dynamics for Dielectric Relaxation
Hilfer, R.
This article summarizes briefly the presentation given by the author at the NATO Advanced Research Workshop on "Broadband Dielectric Spectroscopy and its Advanced Technological Applications", held in Perpignan, France, in September 2011. The purpose of the invited presentation at the workshop was to review and summarize the basic theory of fractional dynamics (Hilfer, Phys Rev E 48:2466, 1993; Hilfer and Anton, Phys Rev E Rapid Commun 51:R848, 1995; Hilfer, Fractals 3(1):211, 1995; Hilfer, Chaos Solitons Fractals 5:1475, 1995; Hilfer, Fractals 3:549, 1995; Hilfer, Physica A 221:89, 1995; Hilfer, On fractional diffusion and its relation with continuous time random walks. In: Pekalski et al. (eds) Anomalous diffusion: from basis to applications. Springer, Berlin, p 77, 1999; Hilfer, Fractional evolution equations and irreversibility. In: Helbing et al. (eds) Traffic and granular flow'99. Springer, Berlin, p 215, 2000; Hilfer, Fractional time evolution. In: Hilfer (ed) Applications of fractional calculus in physics. World Scientific, Singapore, p 87, 2000; Hilfer, Remarks on fractional time. In: Castell and Ischebeck (eds) Time, quantum and information. Springer, Berlin, p 235, 2003; Hilfer, Physica A 329:35, 2003; Hilfer, Threefold introduction to fractional derivatives. In: Klages et al. (eds) Anomalous transport: foundations and applications. Wiley-VCH, Weinheim, pp 17-74, 2008; Hilfer, Foundations of fractional dynamics: a short account. In: Klafter et al. (eds) Fractional dynamics: recent advances. World Scientific, Singapore, p 207, 2011) and demonstrate its relevance and application to broadband dielectric spectroscopy (Hilfer, J Phys Condens Matter 14:2297, 2002; Hilfer, Chem Phys 284:399, 2002; Hilfer, Fractals 11:251, 2003; Hilfer et al., Fractional Calc Appl Anal 12:299, 2009). It was argued, that broadband dielectric spectroscopy might be useful to test effective field theories based on fractional dynamics.
Muon spin relaxation investigation of tetranuclear iron(III) Fe_4(OCH_3)_6(dpm)_6 molecular cluster
Procissi, D.; P. Arosio; Orsini, F.; Marinone, M.; Cornia, A.; Lascialfari, A.
2009-01-01
We present a study of the spin dynamics of Fe_4(OCH_3)_6(dpm)_6 single molecule magnet by means of SQUID magnetization and muon relaxation (µ^(+)SR) measurements. In longitudinal field µ^+SR experiments performed at magnetic fields H=200, 1000 Oe, the muon asymmetry P(t) could be fitted by means of three components, the first constant, the second fast relaxing through a quasiexponential decay, and the third, the slowest relaxing, showing an exponential decay. The slowest muon relaxation rate ...
Schwartz, Benjamin Joel
Femtosecond and picosecond transient absorption spectroscopy are used to probe several fundamental aspects of chemical reactivity in the condensed phase including proton transfer, germinate recombination, isomerization and vibrational relaxation. The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured for the first time, and the effects of external hydrogen-bonding interactions on the proton transfer are studied in detail. The proton transfer takes place in ~240 fsec in non-polar environments, but becomes faster than the instrumental resolution of 110 fsec in methanol solutions. A simple model is proposed to explain these results. The dynamics following photodissociation of CH _2I_2 and other small molecules provide the first direct observations of germinate recombination. The recombination of many different photodissociating species occurs on a ~350 fsec time scale. Results also show that recombination yields but not rates depend on the molecular details of the solvent environment and suggest that recombination kinetics are dominated by a single collision with the surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. The data show no simple correlation between the hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes. This strongly implies that the isomerization of these systems does not provide a suitable testing ground for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in the photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial
Ultraslow dynamics and stress relaxation in the aging of a soft glassy system
Ramos, Laurence; Cipelletti, Luca
2001-01-01
We use linear rheology and multispeckle dynamic light scattering (MDLS) to investigate the aging of a gel composed of multilamellar vesicles. Light scattering data indicate rearrangement of the gel through an unusual ultraslow ballistic motion. A dramatic slowdown of the dynamics with sample age $t_{w}$ is observed for both rheology and MDLS, the characteristic relaxation time scaling as $t_{w}^{\\mu}$. We find the same aging exponent $\\mu =0.78$ for both techniques, suggesting that they probe...
Molecular Dynamics and Picosecond Vibrational Spectra.
1980-07-01
and Identify by block number) molecular dynamics picosecond infra-red spectra crmputer simulation vibrational spectra array processor linear rcsponse...that for molecular dynamics theoretical computation is now long enough, to significantly overlap. This overlap of theory and experiment can, at least...to discover these microscopic atomic trajectories, i.e. the molecular dynamics of solution processes, we must be able to both theoretically compute
Molecular Dynamics in the Vacuum Ultraviolet
1989-01-30
CLASSIFICATION OF THIS PAGE COMPLETED PROJECT SUMMARY TITLE: Molecular dynamics in the Vacuum Ultraviolet PRINCIPAL INVESTIGATOR: Paul L. Houston...DTIC TAB 0 Unannounced 0 By Distr ibution I Availability Codes Avail and I or Dist Special I Molecular Dynamics In the Vacuum Ultraviolet Final Technical...Further development of tunable vacuum ultraviolet sources has opened wide areas of molecular dynamics for study. Completed Research Photodissociation of
Molecular dynamics simulation of benzene
Trumpakaj, Zygmunt; Linde, Bogumił B. J.
2016-03-01
Intermolecular potentials and a few models of intermolecular interaction in liquid benzene are tested by Molecular Dynamics (MD) simulations. The repulsive part of the Lennard-Jones 12-6 (LJ 12-6) potential is too hard, which yields incorrect results. The exp-6 potential with a too hard repulsive term is also often used. Therefore, we took an expa-6 potential with a small Gaussian correction plus electrostatic interactions. This allows to modify the curvature of the potential. The MD simulations are carried out in the temperature range 280-352 K under normal pressure and at experimental density. The Rayleigh scattering of depolarized light is used for comparison. The results of MD simulations are comparable with the experimental values.
Brownian motion from molecular dynamics
Shin, Hyun Kyung; Talkner, Peter; Lee, Eok Kyun
2010-01-01
Brownian motion of single particles with various masses M and diameters D is studied by molecular dynamics simulations. Besides the momentum auto-correlation function of the Brownian particle the memory function and the fluctuating force which enter the generalized Langevin equation of the Brownian particle are determined and their dependence on mass and diameter are investigated for two different fluid densities. Deviations of the fluctuating force distribution from a Gaussian form are observed for small particle diameters. For heavy particles the deviations of the fluctuating force from the total force acting on the Brownian particle decrease linearly with the mass ratio m/M where m denotes the mass of a fluid particle.
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
2010-01-01
The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor ...
Theoretical Concepts in Molecular Photodissociation Dynamics
Henriksen, Niels Engholm
1995-01-01
This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...
Slow dynamics and local quasi-equilibrium-relaxation in supercooled colloidal systems
RubI, J M; SantamarIa-Holek, I; Perez-Madrid, A [Department de Fisica Fonamental, Facultat de Fisica, Universitat de Barcelona, Diagonal 647, 08028 Barcelona (Spain)
2004-06-09
We present a Fokker-Planck description of supercooled colloidal systems exhibiting slow relaxation dynamics. Assuming the existence of a local quasi-equilibrium state during the relaxation of the system, we derive a non-Markovian Fokker-Planck equation for the non-stationary conditional probability. A generalized Stokes-Einstein relation containing the temperature of the system at local quasi-equilibrium instead of the temperature of the bath is obtained. Our results explain experiments showing that the diffusion coefficient is not proportional to the inverse of the effective viscosity at frequencies related to the diffusion timescale.
A preliminary investigation of the dynamic viscoelastic relaxation of bovine cortical bone
Loete T.J.C.
2015-01-01
Full Text Available A new experimental approach is proposed to characterize the dynamic viscoelastic relaxation behaviour of cortical bone. Theoretical models are presented to show that a linear viscoelastic material, when allowed to relax between two long elastic bars, will produce stress, strain and strain rate histories that contain characteristic features. Furthermore, typical experimental results are presented to show that these characteristic features are observed during split Hopkinson bar tests on bovine cortical bone using a Cone-in-Tube striker. The interpretation of this behaviour in the context of a standard linear viscoelastic model is discussed.
Molecular dynamics of membrane proteins.
Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); Crozier, Paul Stewart; Stevens, Mark Jackson
2004-10-01
Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.
Pérez, María Encarnación; Pol, Diego
2012-01-01
Background Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America (“eocardiids”). Results A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. Conclusions The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone. PMID
Programming an Interpreter Using Molecular Dynamics
C.A. Middelburg
2007-01-01
Full Text Available PGA (ProGram Algebra is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily meant for explaining programming language features relating to the use of dynamic data structures, the collection of primitives of molecular dynamics in itself is suited to our programming wants.
2017-01-01
resonance (NMR) Spectral density functions Spin - spin relaxation Molecular dynamics Nuclear Overhauser effect Symmetric top rotor Spin -lattice relaxation...SYMMETRIC TOP ROTOR MODELS AND THE FLEXIBLE SYMMETRIC TOP ROTOR MODEL ECBC-TR-1428 Terry J. Henderson RESEARCH AND TECHNOLOGY DIRECTORATE...Symmetric Top Rotor Models and the Flexible Symmetric Top Rotor Model 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR
Dynamic adjustment: an electoral method for relaxed double proportionality
Linusson, Svante
2013-01-01
We describe an electoral system for distributing seats in a parliament. It gives proportionality for the political parties and close to proportionality for constituencies. The system suggested here is a version of the system used in Sweden and other Nordic countries with permanent seats in each constituency and adjustment seats to give proportionality on the national level. In the national election of 2010 the current Swedish system failed to give proportionality between parties. We examine here one possible cure for this unwanted behavior. The main difference compared to the current Swedish system is that the number of adjustment seats is not fixed, but rather dynamically determined to be as low as possible and still insure proportionality between parties.
Generalized Radon--Nikodym Spectral Approach. Application to Power and Energy Relaxation Dynamics
Bobyl, Aleksandr Vasilievich; Kompan, Mikhail Evgenievich; Malyshkin, Vladislav Gennadievich; Novikova, Olga Valentinovna; Terukova, Ekaterina Evgenievna; Agafonov, Dmitry Valentinovich
2016-01-01
Radon--Nikodym approach to relaxation dynamics, where probability density is built first and then used to calculate observable dynamic characteristic is developed. In contrast with $L^2$ norm approaches, such as Fourier or least squares, this new approach does not use a norm, the problem is reduced to finding the spectrum of an operator (virtual Hamiltonian), which is built in a way that eigenvalues represent the dynamic characteristic of interest and eigenvectors represent probability density. The problems of interpolation and obtaining the distribution of relaxation time from timeserie are considered. Application of the theory is demonstrated on a number of model and experimentally measured (Li-Ion degradation, supercapacitors charge/discharge, etc.) timeseries. Software product, implementing the theory is developed.
Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment
Fujisaki, Hiroshi
2008-01-01
A computational approach to describe the energy relaxation of a high-frequency vibrational mode in a fluctuating heterogeneous environment is outlined. Extending previous work [H. Fujisaki, Y. Zhang, and J.E. Straub, J. Chem. Phys. {\\bf 124}, 144910 (2006)], second-order time-dependent perturbation theory is employed which includes the fluctuations of the parameters in the Hamiltonian within the vibrational adiabatic approximation. This means that the time-dependent vibrational frequencies along an MD trajectory are obtained via a partial geometry optimization of the solute with fixed solvent and a subsequent normal mode calculation. Adopting the amide I mode of N-methylacetamide in heavy water as a test problem, it is shown that the inclusion of dynamic fluctuations may significantly change the vibrational energy relaxation. In particular, it is found that relaxation occurs in two phases, because for short times ($\\lesssim$ 200 fs) the spectral density appears continuous due to the frequency-time uncertainty...
Relaxation dynamics of aftershocks after large volatility shocks in the SSEC index
Mu, Guo-Hua; Zhou, Wei-Xing
2008-09-01
The relaxation dynamics of aftershocks after large volatility shocks are investigated based on two high-frequency data sets of the Shanghai Stock Exchange Composite (SSEC) index. Compared with previous relevant work, we have defined main financial shocks based on large volatilities rather than large crashes. We find that the occurrence rate of aftershocks with the magnitude exceeding a given threshold for both daily volatility (constructed using 1-minute data) and minutely volatility (using intra-minute data) decays as a power law. The power-law relaxation exponent increases with the volatility threshold and is significantly greater than 1. Taking financial volatility as the counterpart of seismic activity, the power-law relaxation in financial volatility deviates remarkably from the Omori law in Geophysics.
Dielectric study on membrane adsorption and release:Relaxation mechanism and diffusion dynamics
LI YuHong; ZHAO KongShuang; HAN Ying
2008-01-01
Dielectric monitoring of the adsorption or release process of salicylic acid (SA) by chitosan membrane shows that the dielectric spectra of the chitosan membrane/SA solution systems change regularly in the adsorption or release process. By analyzing the regularity, a new mechanism for the relaxations is proposed. The concentration polarization layer (CPL) caused by SA adsorption or release is confirmed to be essential for the dielectric relaxations. The changes of the spectra with time are explained by account of the relationship between CPL properties and dielectric strength. Based on this relaxation mechanism, a theoretical method can be established to calculate dynamical parameters of inner structure of the adsorption or release systems from their dielectric spectra. Therefore, dielectric spec-troscopy is demonstrated to be a promising method for estimating interfacial distribution of ionic sub-stances and their binding to membrane in a non-invasive way.
Dielectric study on membrane adsorption and release: Relaxation mechanism and diffusion dynamics
2008-01-01
Dielectric monitoring of the adsorption or release process of salicylic acid (SA) by chitosan membrane shows that the dielectric spectra of the chitosan membrane/ SA solution systems change regularly in the adsorption or release process. By analyzing the regularity, a new mechanism for the relaxations is proposed. The concentration polarization layer (CPL) caused by SA adsorption or release is confirmed to be essential for the dielectric relaxations. The changes of the spectra with time are explained by account of the relationship between CPL properties and dielectric strength. Based on this relaxation mechanism, a theoretical method can be established to calculate dynamical parameters of inner structure of the adsorption or release systems from their dielectric spectra. Therefore, dielectric spec- troscopy is demonstrated to be a promising method for estimating interfacial distribution of ionic sub- stances and their binding to membrane in a non-invasive way.
Phenol-formaldehyde resins: A quantitative NMR study of molecular structure and molecular dynamics
Ottenbourgs, Benjamin Tony
Phenol-formaldehyde (PF) resins have been the subject of this work. 13C liquid-state and solid-state NMR has been used to investigate the molecular structure of mainly novolak and partially of resole resins. 1H wideline in combination with 13C solid-state NMR relaxometry has been applied to study the curing and the molecular dynamics of phenolic resins. It was the intention to provide an insight in the relationship between resin composition, resin structure and subsequent resin properties (by means of the molecular dynamics). An improved 13C liquid-state NMR quantification technique of novolaks in THF-CDCl3 solutions is demonstrated. Full quantitative 13C liquid-state spectra of phenol-formaldehyde resins with high signal- to-noise ratio were obtained by using chromium acetylacetonate under optimized spectral conditions within a few hours spectrometer time. Attached proton test (APT) spectra enabled proper peak assignments in the region with significant overlap. For several novolaks, prepared under different catalytic conditions, the degree of polymerization, degree of branching, number average molecular weight, isomeric distribution, and the number of unreacted ortho and para phenol ring positions was determined with a reduced margin of error, by analyzing and integrating the 13C spectra. The power of 13C solid-state NMR in the analysis of cured PF resins is shown. Particular importance was ascribed to the question of the quantifiability of the experiments when it was desired to measure the degree of conversion by means of a 13C CP/MAS contact time study. The network structure present, and thus also the mechanical properties, is critically dependent upon the final degree of conversion obtained after curing. The degree of conversion, which depended on the cure conditions (cure temperature, cure pressure and cure time), was limited by vitrification as was demonstrated by DSC experiments. Changes in the spin-lattice relaxation time T 1H were observed, providing
Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.
Tavernelli, Ivano
2015-03-17
mechanics (QM/MM) approach has the advantage of providing an atomistic (even though approximated) description of the solvent molecules, which is crucial for the characterization of all ultrafast relaxation phenomena that depend on the geometrical arrangement at the interface between a molecule and the solvent, for example, the hydrogen bond network. After a short description of the TDDFT-based implementation of Ehrenfest and trajectory surface hopping dynamics, I will present applications in different domains of molecular chemistry and physics: the analysis and the understanding of (time-resolved) X-ray absorption spectra, the interpretation of the ultrafast relaxation dynamics of photoexcited dyes in solution, and the design of specific laser pulses (capable of inducing desired chemical reactions) using local control theory.
Conversion of an atomic to a molecular argon ion and low pressure argon relaxation
M, N. Stankov; A, P. Jovanović; V, Lj Marković; S, N. Stamenković
2016-01-01
The dominant process in relaxation of DC glow discharge between two plane parallel electrodes in argon at pressure 200 Pa is analyzed by measuring the breakdown time delay and by analytical and numerical models. By using the approximate analytical model it is found that the relaxation in a range from 20 to 60 ms in afterglow is dominated by ions, produced by atomic-to-molecular conversion of Ar+ ions in the first several milliseconds after the cessation of the discharge. This conversion is confirmed by the presence of double-Gaussian distribution for the formative time delay, as well as conversion maxima in a set of memory curves measured in different conditions. Finally, the numerical one-dimensional (1D) model for determining the number densities of dominant particles in stationary DC glow discharge and two-dimensional (2D) model for the relaxation are used to confirm the previous assumptions and to determine the corresponding collision and transport coefficients of dominant species and processes. Project supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia (Grant No. ON171025).
Madkour, Sherif; Szymoniak, Paulina; Heidari, Mojdeh; von Klitzing, Regine; Schönhals, Andreas
2017-03-01
A combination of nanosized dielectric relaxation (BDS) and thermal spectroscopy (SHS) was utilized to characterize the dynamics of thin films of poly(vinyl methyl ether) (PVME) (thicknesses: 7-160 nm). For the BDS measurements, a recently designed nanostructured electrode system is employed. A thin film is spin-coated on an ultraflat highly conductive silicon wafer serving as the bottom electrode. As top electrode, a highly conductive wafer with nonconducting nanostructured SiO2 nanospacers with heights of 35 or 70 nm is assembled on the bottom electrode. This procedure results in thin supported films with a free polymer/air interface. The BDS measurements show two relaxation processes, which are analyzed unambiguously for thicknesses smaller than 50 nm. The relaxation rates of both processes have different temperature dependencies. One process coincides in its position and temperature dependence with the glassy dynamics of bulk PVME and is ascribed to the dynamic glass transition of a bulk-like layer in the middle of the film. The relaxation rates were found to be thickness independent as confirmed by SHS. Unexpectedly, the relaxation rates of the second process obey an Arrhenius-like temperature dependence. This process was not observed by SHS and was related to the constrained fluctuations in a layer, which is irreversibly adsorbed at the substrate with a heterogeneous structure. Its molecular fluctuations undergo a confinement effect resulting in the localization of the segmental dynamics. To our knowledge, this is the first report on the molecular dynamics of an adsorbed layer in thin films.
Jahur A Mondal; Sandeep Verma; Hirendra N Ghosh; Dipak K Palit
2008-01-01
Relaxation dynamics of the excited singlet states of 2,5-bis-(N-methyl-N-1,3-propdienylaniline)-cyclopentanone (MPAC), a ketocyanine dye, have been investigated using steady-state absorption and emission as well as femtosecond time-resolved absorption spectroscopic techniques. Following photoexcitation using 400 nm light, the molecule is excited to the S2 state, which is fluorescent in rigid matrices at 77 K. S2 state is nearly non-fluorescent in solution and has a very short lifetime (0.5 ± 0.2 ps). In polar aprotic solvents, the S1 state follows a complex multi-exponential relaxation dynamics consisting of torsional motion of the donor groups, solvent re-organization as well as photoisomerization processes. However, in alcoholic solvents, solvent re-organization via intermolecular hydrogen-bonding interaction is the only relaxation process observed in the S1 state. In trifluoroethanol, a strong hydrogen bonding solvent, conversion of the non-hydrogen-bonded form, which is formed following photoexcitation, to the hydrogen-bonded complex has been clearly evident in the relaxation process of the S1 state.
The Role of Rydberg-Valence Coupling in the Ultrafast Relaxation Dynamics of Acetone.
Koch, Markus; Thaler, Bernhard; Heim, Pascal; Ernst, Wolfgang E
2017-08-31
The electronic structure of excited states of acetone is represented by a Rydberg manifold that is coupled to valence states which provide very fast and efficient relaxation pathways. We observe and characterize the transfer of population from photoexcited Rydberg states (6p, 6d, 7s) to a whole series of lower Rydberg states (3p to 4d) and a simultaneous decay of population from these states. We obtain these results with time-resolved photoelectron-photoion coincidence (PEPICO) detection in combination with the application of Bayesian statistics for data analysis. Despite the expectedly complex relaxation behavior, we find that a simple sequential decay model is able to describe the observed PEPICO transients satisfactorily. We obtain a slower decay (∼320 fs) from photoexcited states compared to a faster decay (∼100 fs) of states that are populated by internal conversion, demonstrating that different relaxation dynamics are active. Within the series of Rydberg states populated by internal conversion, the decay dynamics seem to be similar, and a trend of slower decay from lower states indicates an increasingly higher energy barrier along the decay pathway for lower states. The presented results agree all in all with previous relaxation studies within the Rydberg manifold. The state-resolved observation of transient population ranging from 3p to 4d can serve as reference for time-dependent simulations.
Relaxation dynamics of a compressible bilayer vesicle containing highly viscous fluid.
Sachin Krishnan, T V; Okamoto, Ryuichi; Komura, Shigeyuki
2016-12-01
We study the relaxation dynamics of a compressible bilayer vesicle with an asymmetry in the viscosity of the inner and outer fluid medium. First we explore the stability of the vesicle free energy which includes a coupling between the membrane curvature and the local density difference between the two monolayers. Two types of instabilities are identified: a small wavelength instability and a larger wavelength instability. Considering the bulk fluid viscosity and the inter-monolayer friction as the dissipation sources, we next employ Onsager's variational principle to derive the coupled equations both for the membrane and the bulk fluid. The three relaxation modes are coupled to each other due to the bilayer and the spherical structure of the vesicle. Most importantly, a higher fluid viscosity inside the vesicle shifts the crossover mode between the bending and the slipping to a larger value. As the vesicle parameters approach the unstable regions, the relaxation dynamics is dramatically slowed down, and the corresponding mode structure changes significantly. In some limiting cases, our general result reduces to the previously obtained relaxation rates.
Relaxation dynamics of a compressible bilayer vesicle containing highly viscous fluid
Sachin Krishnan, T. V.; Okamoto, Ryuichi; Komura, Shigeyuki
2016-12-01
We study the relaxation dynamics of a compressible bilayer vesicle with an asymmetry in the viscosity of the inner and outer fluid medium. First we explore the stability of the vesicle free energy which includes a coupling between the membrane curvature and the local density difference between the two monolayers. Two types of instabilities are identified: a small wavelength instability and a larger wavelength instability. Considering the bulk fluid viscosity and the inter-monolayer friction as the dissipation sources, we next employ Onsager's variational principle to derive the coupled equations both for the membrane and the bulk fluid. The three relaxation modes are coupled to each other due to the bilayer and the spherical structure of the vesicle. Most importantly, a higher fluid viscosity inside the vesicle shifts the crossover mode between the bending and the slipping to a larger value. As the vesicle parameters approach the unstable regions, the relaxation dynamics is dramatically slowed down, and the corresponding mode structure changes significantly. In some limiting cases, our general result reduces to the previously obtained relaxation rates.
Influence of solid-liquid interactions on dynamic wetting: a molecular dynamics study
Bertrand, Emilie; Blake, Terence D.; De Coninck, Joël
2009-11-01
Large-scale molecular dynamics (MD) simulations of liquid drops spreading on a solid substrate have been carried out for a very wide range of solid-liquid interactions and equilibrium contact angles. The results for these systems are shown to be consistent with the molecular-kinetic theory (MKT) of dynamic wetting, which emphasizes the role of contact-line friction as the principal channel of energy dissipation. Several predictions have been confirmed. These include a quantitative link between the dynamics of wetting and the work of adhesion and the existence of an optimum equilibrium contact angle that maximizes the speed of wetting. A feature of the new work is that key parameters (κ0 and λ), normally accessible only by fitting the MKT to dynamic contact angle data, are also obtained directly from the simulations, with good agreement between the two sources. This validates the MKT at some fundamental level. Further verification is provided by contact angle relaxation studies, which also lend support to the interfacial tension relaxation process invoked in Shikhmurzaev's hydrodynamic model of dynamic wetting.
Vizcaíno Sergio F
2004-04-01
Full Text Available Abstract Background Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have shaped the evolutionary history of diverse terrestrial organisms. Living xenarthrans (armadillos, anteaters and sloths constitute an ideal model for studying the influence of past environmental changes on species diversification. Indeed, extant xenarthran species are relicts from an evolutionary radiation enhanced by their isolation in South America during the Tertiary era, a period for which major climate variations and tectonic events are relatively well documented. Results We applied a Bayesian approach to three nuclear genes in order to relax the molecular clock assumption while accounting for differences in evolutionary dynamics among genes and incorporating paleontological uncertainties. We obtained a molecular time scale for the evolution of extant xenarthrans and other placental mammals. Divergence time estimates provide substantial evidence for contemporaneous diversification events among independent xenarthran lineages. This correlated pattern of diversification might possibly relate to major environmental changes that occurred in South America during the Cenozoic. Conclusions The observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans. Our findings open ways to test this hypothesis further in other South American mammalian endemics like hystricognath rodents, platyrrhine primates, and didelphid marsupials.
Borlaug, Barry A; Jaber, Wissam A; Ommen, Steve R; Lam, Carolyn S P; Redfield, Margaret M; Nishimura, Rick A
2011-06-01
Recent studies have examined haemodynamic changes with stressors such as isometric handgrip and rapid atrial pacing in heart failure with preserved ejection fraction (HFpEF), but little is known regarding left ventricular (LV) pressure-volume responses during dynamic exercise. To assess LV haemodynamic responses to dynamic exercise in patients with HFpEF. Twenty subjects with normal ejection fraction (EF) and exertional dyspnoea underwent invasive haemodynamic assessment during dynamic exercise to evaluate suspected HFpEF. LV end-diastolic pressure was elevated at rest (>15 mm Hg, n=18) and with exercise (≥20 mm Hg, n=20) in all subjects, consistent with HFpEF. Heart rate (HR), blood pressure, arterial elastance and cardiac output increased with exercise (all pincreased by 43-56% with exercise (both pincreases in HR and the proportion of diastole that elapsed prior to estimated complete relaxation increased (pincreased 50% during exercise (p=0.0003). Exercise increases in LV filling pressures correlated with changes in diastolic relaxation rates, chamber stiffness and arterial afterload but were not related to alterations in preload volume, HR or cardiac output. In patients with newly diagnosed HFpEF, LV filling pressures increase during dynamic exercise in association with inadequate enhancement of relaxation and acute increases in LV chamber stiffness. Therapies that enhance diastolic reserve function may improve symptoms of exertional intolerance in patients with hypertensive heart disease and early HFpEF.
Dynamical theory of spin noise and relaxation - prospects for real time NMR measurements
Field, Timothy
2014-03-01
The dynamics of a spin system is usually calculated using the density matrix. However, the usual formulation in terms of the density matrix predicts that the signal will decay to zero, and does not address the stochastic dynamics of individual spins. Spin fluctuations are to be viewed as an intrinsic quantum mechanical property of such systems immersed in random magnetic environments, and are observed as ``spin noise'' in the absence of any radio frequency (RF) excitation. Using stochastic calculus we develop a dynamical theory of spin noise and relaxation whose origins lie in the component spin fluctuations. This entails consideration of random pure states for individual protons, and how these pure states are correctly combined when the density matrix is formulated. Both the lattice and the spins are treated quantum mechanically. Such treatment incorporates both the processes of spin-spin and (finite temperature) spin-lattice relaxation. Our results reveal the intimate connections between spin noise and conventional spin relaxation, in terms of a modified spin density (MSD), distinct from the density matrix, which is necessary to describe non-ensemble averaged properties of spin systems. With the prospect of ultra-fast digitization, the role of spin noise in real time parameter extraction for (NMR) spin systems, and the advantage over standard techniques, is of essential importance, especially for systems containing a small number of spins. In this presentation we outline prospects for harnessing the recent dynamical theory in terms of spin noise measurement, with attention to real time properties.
Folk, R; Holovatch, Yu; Moser, G
2009-03-01
We calculate the relaxational dynamical critical behavior of systems of O(n_{ parallel}) plus sign in circleO(n_{ perpendicular}) symmetry including conservation of magnetization by renormalization group theory within the minimal subtraction scheme in two-loop order. Within the stability region of the Heisenberg fixed point and the biconical fixed point, strong dynamical scaling holds, with the asymptotic dynamical critical exponent z=2varphinu-1 , where varphi is the crossover exponent and nu the exponent of the correlation length. The critical dynamics at n_{ parallel}=1 and n_{ perpendicular}=2 is governed by a small dynamical transient exponent leading to nonuniversal nonasymptotic dynamical behavior. This may be seen, e.g., in the temperature dependence of the magnetic transport coefficients.
Microphase structures and 13C NMR relaxation parameters in ultrahigh molecular weight polyethylene
朱清仁; 洪昆仑; 鲁非; 戚嵘嵘; 庞文民; 周贵恩; 宋名实
1995-01-01
The phase transformations in ultrahigh molecular weight polyethylene（UHMWPE）gel-filmsupon superdrawing have been studied by X-ray diffraction and high resolution solid state 13C NMR.Themorphological change and molecular motions in the crystalline phase,amorphous phase and interphase are dis-cussed according to the 13C nuclear relaxation time(T1c,T2cresults.A brief interpretation to the three orfour T1cvalues in the crystalline phase is presented.It is found that the component with the highest T1c(T1cα)plays a key role in the forming of ’Shish-Kebab’ microfibril which determines the sample strength andmodulus,namely,the greater the T1cα,the higher the modulus and strength of the drawn UHMWPEgel-film.These results support the ’Shish-Kebabs’ model in crystalline polymers.
The Plastic and Liquid Phases of CCl$_3$Br Studied by Molecular Dynamics Simulations
Caballero, Nirvana; Carignano, Marcelo; Serra, Pablo
2013-01-01
We present a molecular dynamics study of the liquid and plastic crystalline phases of CCl$_3$Br. We investigated the short-range orientational order using a recently developed classification method and we found that both phases behave in a very similar way. The only differences occur at very short molecular separations, which are shown to be very rare. The rotational dynamics was explored using time correlation functions of the molecular bonds. We found that the relaxation dynamics corresponds to an isotropic diffusive mode for the liquid phase, but departs from this behavior as the temperature is decreased and the system transitions into the plastic phase.
Molecular View on Supramolecular Chain and Association Dynamics
Monkenbusch, M.; Krutyeva, M.; Pyckhout-Hintzen, W.; Antonius, W.; Hövelmann, C. H.; Allgaier, J.; Brás, A.; Farago, B.; Wischnewski, A.; Richter, D.
2016-09-01
The chain and association dynamics of supramolecular polymer ensembles decisively determines their properties. Using neutron spin echo (NSE) spectroscopy we present molecular insight into the space and time evolution of this dynamics. Studying a well characterized ensemble of linearly associating telechelic poly(ethylene glycol) melts carrying triple H-bonding end groups, we show that H-bond breaking significantly impacts the mode spectrum of the associates. The breaking affects the mode contributions and not the relaxation times as was assumed previously. NSE spectra directly reveal the so far intangible H-bond lifetimes in the supramolecular melt and demonstrate that for both the microscopic and the macroscopic dynamics of the supramolecular ensemble the instantaneous average of the Mw distribution governs the system response at least as long as the Rouse picture applies.
The dynamical activation-relaxation technique (DART): an on-the-fly kinetic Monte-Carlo algorithm
El-Mellouhi, Fadwa; Cote, Michel; Lewis, Laurent J.; Mousseau, Normand
2008-03-01
We present DART, the dynamical activation-relaxation technique, that combines the activation-relaxation technique (ART nouveau) with a non-lattice KMC method that allows the on-the-fly identification of barriers and the full treatment of lattice deformations. Most KMC schemes rely on the use of a fixed list of events and barriers, which are drawn with the proper weight during the simulation. While this works well for a number of problems (such as metal-on-metal growth), it cannot be used for processes where the events may change with time. DART overcomes this limitation. ART nouveau has been used extensively for the study of activated mechanisms in different materials within both an empirical and an ab-initio description of the systems. In the DART implementation, KMC moves are based on a catalog of events constructed on-the-fly using ART. After each KMC move, this catalog is updated so as to take into account new environments that may appear. A topological description of the structure of the system at each moment allows the method to identify rapidly these new environments and to move forward efficiently. In this talk, we will describe the method and present the case of interstitial diffusion in Si. Our results are compared with previous molecular-dynamics and on-lattice KMC simulations.
Programming an interpreter using molecular dynamics
2008-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primari...
Programming an Interpreter Using Molecular Dynamics
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in programming.We consider the programming of an interpreter for a program notation that is close to existing assembly languages using PGA with the primitives of molecular dynamics as basic instructions. It happens that, although primarily...
Relaxation dynamics and exciton energy transfer in the low-temperature phase of MEH-PPV
Consani, Cristina; Koch, Federico [Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg (Germany); Panzer, Fabian; Unger, Thomas; Köhler, Anna [Lehrstuhl Experimentalphysik II, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth (Germany); Brixner, Tobias, E-mail: brixner@phys-chemie.uni-wuerzburg.de [Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg (Germany); Center for Nanosystems Chemistry (CNC), Universität Würzburg, Am Hubland, 97074 Würzburg (Germany)
2015-06-07
Understanding the effects of aggregation on exciton relaxation and energy transfer is relevant to control photoinduced function in organic electronics and photovoltaics. Here, we explore the photoinduced dynamics in the low-temperature aggregated phase of a conjugated polymer by transient absorption and coherent electronic two-dimensional (2D) spectroscopy. Coherent 2D spectroscopy allows observing couplings among photoexcited states and discriminating band shifts from homogeneous broadening, additionally accessing the ultrafast dynamics at various excitation energies simultaneously with high spectral resolution. By combining the results of the two techniques, we differentiate between an initial exciton relaxation, which is not characterized by significant exciton mobility, and energy transport between different chromophores in the aggregate.
The spin-temperature theory of dynamic nuclear polarization and nuclear spin-lattice relaxation
Byvik, C. E.; Wollan, D. S.
1974-01-01
A detailed derivation of the equations governing dynamic nuclear polarization (DNP) and nuclear spin lattice relaxation by use of the spin temperature theory has been carried to second order in a perturbation expansion of the density matrix. Nuclear spin diffusion in the rapid diffusion limit and the effects of the coupling of the electron dipole-dipole reservoir (EDDR) with the nuclear spins are incorporated. The complete expression for the dynamic nuclear polarization has been derived and then examined in detail for the limit of well resolved solid effect transitions. Exactly at the solid effect transition peaks, the conventional solid-effect DNP results are obtained, but with EDDR effects on the nuclear relaxation and DNP leakage factor included. Explicit EDDR contributions to DNP are discussed, and a new DNP effect is predicted.
Low Parametric Sensitivity Realizations with relaxed L2-dynamic-range-scaling constraints
Hilaire, Thibault
2009-01-01
This paper presents a new dynamic-range scaling for the implementation of filters/controllers in state-space form. Relaxing the classical L2-scaling constraints by specific fixed-point considerations allows for a higher degree of freedom for the optimal L2-parametric sensitivity problem. However, overflows in the implementation are still prevented. The underlying constrained problem is converted into an unconstrained problem for which a solution can be provided. This leads to realizations whi...
Improved dynamical scaling analysis using the kernel method for nonequilibrium relaxation.
Echinaka, Yuki; Ozeki, Yukiyasu
2016-10-01
The dynamical scaling analysis for the Kosterlitz-Thouless transition in the nonequilibrium relaxation method is improved by the use of Bayesian statistics and the kernel method. This allows data to be fitted to a scaling function without using any parametric model function, which makes the results more reliable and reproducible and enables automatic and faster parameter estimation. Applying this method, the bootstrap method is introduced and a numerical discrimination for the transition type is proposed.
Low Parametric Sensitivity Realizations with relaxed L2-dynamic-range-scaling constraints
Hilaire, Thibault
2009-01-01
This paper presents a new dynamic-range scaling for the implementation of filters/controllers in state-space form. Relaxing the classical L2-scaling constraints by specific fixed-point considerations allows for a higher degree of freedom for the optimal L2-parametric sensitivity problem. However, overflows in the implementation are still prevented. The underlying constrained problem is converted into an unconstrained problem for which a solution can be provided. This leads to realizations whi...
Turton, David A; Sonnleitner, Thomas; Ortner, Alex; Walther, Markus; Hefter, Glenn; Seddon, Kenneth R; Stana, Simona; Plechkova, Natalia V; Buchner, Richard; Wynne, Klaas
2012-01-01
The structure and dynamics of ionic liquids (ILs) are unusual due to the strong interactions between the ions and counter ions. These microscopic properties determine the bulk transport properties critical to applications of ILs such as advanced fuel cells. The terahertz dynamics and slower relaxations of simple alkylammonium nitrate protic ionic liquids (PILs) are here studied using femtosecond optical Kerr-effect spectroscopy, dielectric relaxation spectroscopy, and terahertz time-domain spectroscopy. The observed dynamics give insight into more general liquid behaviour while comparison with glass-forming liquids reveals an underlying power-law decay and relaxation rates suggest supramolecular structure and nanoscale segregation.
R J Sengwa; Sonu Sankhila
2006-08-01
Dielectric relaxation study of the binary mixtures of poly(vinyl pyrrolidone) (PVP) (Mw = 24000, 40000 and 360000 g mol-1) with ethyl alcohol (EA) and poly(ethylene glycol)s (PEGs) (Mw = 200 and 400 g mol-1) in dilute solutions of dioxane were carried out at 10.1 GHz and 35°} C. The relaxation time of PVP–EA mixtures was interpreted by the consideration of a wait-and-switch model in the local structure of self-associated ethyl alcohol molecules and also the PVP chain length as a geometric constraint for the reorientational motion of ethyl alcohol molecules. The formation of complexes and effect of PVP chain length on the molecular dynamics, chain flexibility and stretching of PEG molecules in PVP–PEG mixtures were explored from the comparative values of dielectric relaxation time. Further, relaxation time values in dioxane and benzene solvent confirm the viscosity independent molecular dynamics in PVP–EA mixtures but the values vary significantly with the non-polar solvent environment.
Thermally driven molecular linear motors - A molecular dynamics study
Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence
2009-01-01
We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled...
Scaling of Langevin and molecular dynamics persistence times of nonhomogeneous fluids.
Olivares-Rivas, Wilmer; Colmenares, Pedro J
2012-01-01
The existing solution for the Langevin equation of an anisotropic fluid allowed the evaluation of the position-dependent perpendicular and parallel diffusion coefficients, using molecular dynamics data. However, the time scale of the Langevin dynamics and molecular dynamics are different and an ansatz for the persistence probability relaxation time was needed. Here we show how the solution for the average persistence probability obtained from the backward Smoluchowski-Fokker-Planck equation (SE), associated to the Langevin dynamics, scales with the corresponding molecular dynamics quantity. Our SE perpendicular persistence time is evaluated in terms of simple integrals over the equilibrium local density. When properly scaled by the perpendicular diffusion coefficient, it gives a good match with that obtained from molecular dynamics.
Ponzoni, Stefano
2014-10-16
By properly tuning the photon energy of a femtosecond laser pump, we disentangle, in carbon nanotube-Si (CNT/Si) heterojunctions, the fast relaxation dynamics occurring in CNT from the slow repopulation dynamics due to hole charge transfer at the junction. In this way we are able to track the transfer of the photogenerated holes from the Si depletion layer to the CNT layer, under the action of the built-in heterojunction potential. This also clarifies that CNT play an active role in the junction and do not act only as channels for charge collection and transport.
Yoshioka, Sumie; Aso, Yukio; Osako, Tsutomu; Kawanishi, Toru
2008-10-01
In order to examine the possibility of determining the molecular mobility of hydration water in active pharmaceutical ingredient (API) hydrates by NMR relaxation measurement, spin-spin relaxation and spin-lattice relaxation were measured for the 11 API hydrates listed in the Japanese Pharmacopeia using pulsed (1)H-NMR. For hydration water that has relatively high mobility and shows Lorentzian decay, molecular mobility as determined by spin-spin relaxation time (T(2)) was correlated with ease of evaporation under both nonisothermal and isothermal conditions, as determined by DSC and water vapor sorption isotherm analysis, respectively. Thus, T(2) may be considered a useful parameter which indicates the molecular mobility of hydration water. In contrast, for hydration water that has low mobility and shows Gaussian decay, T(2) was found not to correlate with ease of evaporation under nonisothermal conditions, which suggests that in this case, the molecular mobility of hydration water was too low to be determined by T(2). A wide range of water mobilities was found among API hydrates, from low mobility that could not be evaluated by NMR relaxation time, such as that of the water molecules in pipemidic acid hydrate, to high mobility that could be evaluated by this method, such as that of the water molecules in ceftazidime hydrate. (c) 2008 Wiley-Liss, Inc. and the American Pharmacists Association
Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio
2017-02-22
Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.
Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio
2017-01-01
Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation. PMID:28223697
Greene, Patrick T.; Schofield, Samuel P.; Nourgaliev, Robert
2017-04-01
A new mesh smoothing method designed to cluster cells near a dynamically evolving interface is presented. The method is based on weighted condition number mesh relaxation with the weight function computed from a level set representation of the interface. The weight function is expressed as a Taylor series based discontinuous Galerkin projection, which makes the computation of the derivatives of the weight function needed during the condition number optimization process a trivial matter. For cases when a level set is not available, a fast method for generating a low-order level set from discrete cell-centered fields, such as a volume fraction or index function, is provided. Results show that the low-order level set works equally well as the actual level set for mesh smoothing. Meshes generated for a number of interface geometries are presented, including cases with multiple level sets. Dynamic cases with moving interfaces show the new method is capable of maintaining a desired resolution near the interface with an acceptable number of relaxation iterations per time step, which demonstrates the method's potential to be used as a mesh relaxer for arbitrary Lagrangian Eulerian (ALE) methods.
Greene, Patrick; Schofield, Sam; Nourgaliev, Robert
2016-11-01
A new mesh smoothing method designed to cluster cells near a dynamically evolving interface is presented. The method is based on weighted condition number mesh relaxation with the weight function being computed from a level set representation of the interface. The weight function is expressed as a Taylor series based discontinuous Galerkin (DG) projection, which makes the computation of the derivatives of the weight function needed during the condition number optimization process a trivial matter. For cases when a level set is not available, a fast method for generating a low-order level set from discrete cell-centered fields, such as a volume fraction or index function, is provided. Results show that the low-order level set works equally well for the weight function as the actual level set. The method retains the excellent smoothing capabilities of condition number relaxation, while providing a method for clustering mesh cells near regions of interest. Dynamic cases for moving interfaces are presented to demonstrate the method's potential usefulness as a mesh relaxer for arbitrary Lagrangian Eulerian (ALE) methods. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Multi-probe relaxation dispersion measurements increase sensitivity to protein dynamics.
Fenwick, R Bryn; Oyen, David; Wright, Peter E
2016-02-17
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements are a valuable tool for the characterization of structural transitions on the micro-millisecond timescale. While the measurement of (15)N relaxation dispersion is now routine, the measurements with alternative nuclei remain limited. Here we report (15)N as well as (1)H R2 relaxation dispersion measurements of the N23PP/S148A "dynamic knockout" mutant of dihydrofolate reductase. The (1)H dispersion measurements are complementary to (15)N data as many additional residues are observed to have dispersive behavior for the (1)H nucleus. Simultaneous fitting of the dispersion profiles for the two nuclei increases the accuracy of exchange parameters determined for individual residues and clustered groups of residues. The different sensitivity of the two nuclei to changes in backbone torsional angles, ring currents, and hydrogen bonding effects provides important insights into the nature of the structural changes that take place during the exchange process. We observe clear evidence of direct and indirect hydrogen bond effects for the (15)N and (1)H chemical shift changes in the active-site, modulation of ring current shielding in the CD-loop and backbone torsional changes in a cluster of residues associated with the C-terminus. This work demonstrates the power of combined (1)H and (15)N probes for the study of backbone dynamics on the micro-millisecond timescale though the analysis of chemical shift changes.
Molecular dynamics simulations of non-Fourier heat conduction
2008-01-01
Unsteady heat conduction is known to deviate significantly from Fourier's law when the system time and length scales are within certain temporal and spatial windows of relaxation. Classical molecular dynamics simulations were used to investigate unsteady heat conduction in argon thin films with a sudden temperature increase or heat flux at one surface to study the non-Fourier heat conduction effects in argon thin films. The studies were conducted with both pure argon films and films with vacancy defects. The temperature pro- files in the argon films showed the existence of mechanical waves when the thin film was suddenly heated and the wave nature of the heat propagation. The flux phase relaxation time, τq, and the temperature phase relaxation time, τq were calculated from the temporal vari- ations of the energy flux and temperature distribution in the film. Comparisons of the MD temperature profiles with temperature profiles predicted by Fourier's law show that Fourier's law is not able to predict the temperature variations with time. Different film thicknesses were also studied to illustrate the variation of the time needed for the films to reach steady-state temperature profiles after a sudden tem- perature rise at one surface and to illustrate the finite speed of the energy waves.
Lu, Wei; Liu, Xuefeng; Lu, Hong; Li, Caizhen; Lai, Jiawei; Zhao, Chuan; Tian, Ye; Liao, Zhimin; Jia, Shuang; Sun, Dong
2016-01-01
Three dimensional (3D) Dirac semimetal exhibiting ultrahigh mobility has recently attracted enormous research interests as 3D analogues of graphene. From the prospects of future application toward electronic/optoelectronic devices with extreme performance, it is crucial to understand the relaxation dynamics of photo-excited carriers and their coupling with lattice. In this work, we report ultrafast transient reflection measurements of photo-excited carrier dynamics in cadmium arsenide (Cd3As2), which is among the most stable Dirac semimetals that have been confirmed experimentally. With low energy probe photon of 0.3 eV, photo-excited Dirac Fermions dynamics closing to Dirac point are probed. Through transient reflection measurements on bulk and nanoplate samples that have different doping intensities, and systematic probe wavelength, pump power and lattice temperature dependent measurements, the dynamical evolution of carrier distributions can be retrieved qualitatively using a two-temperature model. The pho...
Histidine side-chain dynamics and protonation monitored by C-13 CPMG NMR relaxation dispersion
Hass, M. A. S.; Yilmaz, A.; Christensen, Hans Erik Mølager;
2009-01-01
The use of C-13 NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically C-13 labeled histidine residues in plastocyanin (PCu) from...... Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for C-13(epsilon 1) nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from...... or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the C-13(epsilon 1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains...
A subzero 1H NMR relaxation investigation of water dynamics in tomato pericarp.
Foucat, Loïc; Lahaye, Marc
2014-09-01
(1)H NMR relaxation times (T1 and T2) were measured at low field (0.47 T) in pericarp tissues of three tomato genotypes (Ferum, LA0147 and Levovil) at subzero temperature (-20 °C) and two ripening stages (mature green and red). The unfrozen water dynamics was characterised by two T1 and three T2 components. The relaxation time values and their associated relative populations allowed differentiating the ripening stage of only LA0147 and Levovil lines. But the three genotypes were unequivocally discriminated at the red ripe stage. The unfrozen water distribution was discussed in terms of specific interactions, especially with sugars, in relation with their osmoprotectant effects.
Femtosecond Transient Absorption Spectra and Relaxation Dynamics of SWNT in SDS Micellar Solutions
Nadtochenko, V. A.; Lobach, A. S.; Gostev, F. E.; Tcherbinin, D. O.; Sobennikov, A.; Sarkisov, O. M.
2005-09-01
Transient absorption spectra and relaxation dynamics of excited SWNT were studied by femtosecond absorption spectroscopy as a function of: the energy of excitation quanta (ℏω = 2 eV, 2.5 eV, 4 eV); the density of the excitation energy; polarizations of the pump and probe pulses. The transient absorption spectra were monitored by white supercontinuum light pulse in the spectral region of ˜ 1.2 ÷ 3.6 eV. The induced transient absorption spectra of SWNT are considered as filling of the size-quantized energy bands with nonequilibrium carriers; renormalization of the one-dimensional energy bands at high density of the induced plasma; quantum confined Stark effect and screening of excitons. The anisotropic relaxation rate is observed.
Ishii, Masashi
2010-09-01
For dynamic analyses of a polymer surface, a dielectric relaxation measurement technique with parallel electrodes placed away from the surface was developed. In this technique, a liquid heating medium was filled in the space between the polymer surface and the electrodes. The construction that maintains the surface can clarify the physical interactions between the liquid and the bare surface and controlling the temperature of the liquid reveals the thermal activation property of the surface. The dielectric relaxation spectrum of the surface convoluted into the bulk and liquid spectra can be obtained by a reactance analysis and the surface spectrum is expressed with an equivalent resistance-capacitance parallel circuit. On the basis of the electromechanical analogy, the electric elements can be converted into mechanical elements that indicate the viscoelasticity of the polymer surface. Using these measurement and analysis techniques, the electric and mechanical properties of the surface of a gelatinized chloroprene rubber sample were analyzed.
Relaxation dynamics of a polymer network modeled by a multihierarchical structure.
Jurjiu, A; Volta, A; Beu, T
2011-07-01
We numerically analyze the scaling behavior of experimentally accessible dynamical relaxation forms for polymer networks modeled by a finite multihierarchical structure. In the framework of generalized Gaussian structures, by making use of the eigenvalue spectrum of the connectivity matrix, we determine the averaged monomer displacement under local external forces as well as the mechanical relaxation quantities (storage and loss moduli). Hence we generalize the known analysis for both classes of fractals to the case of multihierarchical structure, for which even though we have a mixed growth algorithm, the above cited observables still give information about the two different underlying topologies. For very large lattices, reached via an algebraic procedure that avoids the numerical diagonalizations of the corresponding connectivity matrices, we depict the scaling of both component fractals in the intermediate time (frequency) domain, which manifests two different slopes.
Dynamical processes in atomic and molecular physics
Ogurtsov, Gennadi
2012-01-01
Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece
HTMD: High-Throughput Molecular Dynamics for Molecular Discovery.
Doerr, S; Harvey, M J; Noé, Frank; De Fabritiis, G
2016-04-12
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features.
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
Volkovich, Roie
2010-01-01
The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor molecular junction model yields currents which transfer charge (electron and holes) unevenly to the two leads in the absence of a bias potential. The utility of this mechanism for charge pumping in steady state conditions is proposed.
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Modeling the Hydrogen Bond within Molecular Dynamics
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular Dynamics Simulations of Simple Liquids
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Structural Dynamics of the Potassium Channel Blocker ShK: SRLS Analysis of (15)N Relaxation.
Meirovitch, Eva; Tchaicheeyan, Oren; Sher, Inbal; Norton, Raymond S; Chill, Jordan H
2015-12-10
The 35-residue ShK peptide binds with high affinity to voltage-gated potassium channels. The dynamics of the binding surface was studied recently with (microsecond to millisecond) (15)N relaxation dispersion and (picosecond to nanosecond) (15)N spin relaxation of the N-H bonds. Relaxation dispersion revealed microsecond conformational-exchange-mediated exposure of the functionally important Y23 side chain to the peptide surface. The spin relaxation parameters acquired at 14.1 and 16.45 T have been subjected to model-free (MF) analysis, which yielded a squared generalized order parameter, S(2), of approximately 0.85 for virtually all of the N-H bonds. Only a "rigid backbone" evaluation could be inferred. We ascribe this limited information to the simplicity of MF in the context of challenging data. To improve the analysis, we apply the slowly relaxing local structure (SRLS) approach, which is a generalization of MF. SRLS describes N-H bond dynamics in ShK in terms of a local potential, u, ranging from 10 to 18.5 kBT, and a local diffusion rate, D2, ranging from 4.2 × 10(8) to 2.4 × 10(10) s(-1). This analysis shows that u is outstandingly strong for Y23 and relatively weak for K22, whereas D2 is slow for Y23 and fast for K22. These observations are relevant functionally because of the key role of the K22-Y23 dyad in ShK binding to potassium channels. The disulfide-bond network exhibits a medium-strength potential and an alternating wave-like D2 pattern. This is indicative of moderate structural restraints and motional plasticity, in support of, although not directly correlated with, the microsecond binding-related conformational exchange process detected previously. Thus, new information on functionally important residues in ShK and its overall conformational stability emerged from the SRLS analysis, as compared with the previous MF-based estimate of backbone dynamics as backbone rigidity.
Dynamics of Star Polymers in Fast Extensional Flow and Stress Relaxation
Huang, Qian; Agostini, Serena; Hengeller, Ludovica;
2016-01-01
We confirm the observation from Ianniruberto and Marrucci [ Macromolecules 2013, 46, 267-275 ] that entangled melts of branched polystyrenes behave like linear polystyrenes in the steady state of fast extensional flow, by measuring a linear, an asymmetric star, and a symmetric star polystyrene...... with the same span molecular weight (180 kg/mol). We show that all three melts reach the same extensional steady-state viscosity in fast extensional flow (faster than the inverse Rouse time). We further measure stress relaxation following steady extensional flow for the three melts. We show that initially...
Molecular dynamics studies of entangled polymer chains
Bulacu, Monica Iulia
2008-01-01
The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a
A thread calculus with molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2010-01-01
We present a theory of threads, interleaving of threads, and interaction between threads and services with features of molecular dynamics, a model of computation that bears on computations in which dynamic data structures are involved. Threads can interact with services of which the states consist o
Programming an interpreter using molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the programmi
Programming an interpreter using molecular dynamics
Bergstra, J.A.; Middelburg, C.A.
2007-01-01
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of \\PGA, which bears on the use of dynamic data structures in programming. We consider the
Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)
2015-06-28
In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible
Lerbret, A; Affouard, F; Hedoux, A; Guinet, Y; Descamps, M
2007-01-01
The influence of three well-known disaccharides, namely trehalose, maltose and sucrose, on some structural and dynamical properties of lysozyme has been investigated by means of molecular dynamics computer simulations in the 37-60 wt % concentration range. The effects of sugars on the protein conformation are found relatively weak, in agreement with the preferential hydration of lysozyme. Conversely, sugars seem to increase significantly the relaxation times of the protein. These effects are shown to be correlated to the fractional solvent accessibilities of lysozyme residues and further support the slaving of protein dynamics. Moreover, a significant increase in the relaxation times of lysozyme, sugars and water molecules is observed within the studied concentration range and may result from the percolation of the hydrogen-bond network of sugar molecules. This percolation appears to be of primary importance to explain the influence of sugars on the dynamical properties of lysozyme and water.
Bhabani S Mallik; Amalendu Chandra
2012-01-01
We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (∼80 fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (∼1.3 ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (∼12 ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations.
Modeling hybrid perovskites by molecular dynamics.
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Modeling hybrid perovskites by molecular dynamics
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Molecular Dynamics Studies of Matrix Metalloproteases.
Díaz, Natalia; Suárez, Dimas
2017-01-01
Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.
Dynamic molecular crystals with switchable physical properties.
Sato, Osamu
2016-06-21
The development of molecular materials whose physical properties can be controlled by external stimuli - such as light, electric field, temperature, and pressure - has recently attracted much attention owing to their potential applications in molecular devices. There are a number of ways to alter the physical properties of crystalline materials. These include the modulation of the spin and redox states of the crystal's components, or the incorporation within the crystalline lattice of tunable molecules that exhibit stimuli-induced changes in their molecular structure. A switching behaviour can also be induced by changing the molecular orientation of the crystal's components, even in cases where the overall molecular structure is not affected. Controlling intermolecular interactions within a molecular material is also an effective tool to modulate its physical properties. This Review discusses recent advances in the development of such stimuli-responsive, switchable crystalline compounds - referred to here as dynamic molecular crystals - and suggests how different approaches can serve to prepare functional materials.
Electronic relaxation dynamics of PCDA-PDA studied by transient absorption spectroscopy.
Joung, Joonyoung F; Baek, Junwoo; Kim, Youngseo; Lee, Songyi; Kim, Myung Hwa; Yoon, Juyoung; Park, Sungnam
2016-08-17
Photo-curable polymers originating from 10,12-pentacosadiynoic acid (PCDA-PDA) are commonly used polydiacetylenes (PDAs). PCDA-PDA exhibits thermochromic properties undergoing a unique colorimetric transition from blue to red as the temperature is increased from low to high. In this work, we have carefully studied the temperature-dependent optical properties of PCDA-PDA by using UV-visible absorption, FTIR, Raman, and transient absorption (TA) spectroscopy in combination with quantum chemical calculations. Temperature-dependent UV-visible absorption spectra indicate that PCDA-PDA exhibits reversible thermochromic properties up to 60 °C and its thermochromic properties become irreversible above 60 °C. Such distinct thermochromic properties are also manifested in TA signals so that the electronically excited PCDA-PDA relaxes to the ground state via an intermediate state at 20 °C (blue form) but it relaxes directly back to the ground state at 80 °C (red form). The electronic relaxation dynamics of PCDA-PDA are comprehensively analyzed based on different kinetic models by using the global fitting analysis method. The intermediate state in the blue form of PCDA-PDA is clearly found to be responsible for fluorescence quenching. FTIR and Raman spectroscopy and quantum chemical calculations confirm that the H-bonds between the carboxylic acid groups in PCDA-PDA are broken at high temperatures leading to an irreversible structural change of PCDA-PDA.
Histidine side-chain dynamics and protonation monitored by {sup 13}C CPMG NMR relaxation dispersion
Hass, Mathias A. S. [Leiden University, Institute of Chemistry (Netherlands); Yilmaz, Ali [University of Copenhagen, Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences (Denmark); Christensen, Hans E. M. [Technical University of Denmark, Department of Chemistry (Denmark); Led, Jens J. [University of Copenhagen, Department of Chemistry (Denmark)], E-mail: led@kiku.dk
2009-08-15
The use of {sup 13}C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically {sup 13}C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for {sup 13}C{sup {epsilon}}{sup 1} nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from {sup 15}N backbone relaxation measurements. Compared to measurements of backbone nuclei, {sup 13}C{sup {epsilon}}{sup 1} dispersion provides a more direct method to monitor interchanging protonation states or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the {sup 13}C{sup {epsilon}}{sup 1} dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed.
Metal Atom Dynamics and Spin-Lattice Relaxation in Multilayer Sandwich Compounds
Nowik, Israel; Herber, Rolfe H., E-mail: HERBER@VMS.HUJI.AC.il [Hebrew University of Jerusalem, Racah Institute of Physics (Israel)
2004-12-15
Temperature-dependent {sup 57}Fe Moessbauer spectroscopy has been used to elucidate the hyperfine parameters and dynamical behavior of the metal atom in several organo-iron complexes which have one or more {eta}{sup 5} P{sub 5} ring structures as ligated groups. The spin-lattice relaxation of the (paramagnetic) one-electron oxidation products occurs on a time scale fast compared to {tau}{sub 1/2} (ME) at temperatures in the range 85 < T < 320 K.
Davies, H. C.; Turner, R. E.
1977-01-01
A dynamical relaxation technique for updating prediction models is analyzed with the help of the linear and nonlinear barotropic primitive equations. It is assumed that a complete four-dimensional time history of some prescribed subset of the meteorological variables is known. The rate of adaptation of the flow variables toward the true state is determined for a linearized f-model, and for mid-latitude and equatorial beta-plane models. The results of the analysis are corroborated by numerical experiments with the nonlinear shallow-water equations.
Alexandrov, Nikola A; Marinova, Krastanka G; Gurkov, Theodor D; Danov, Krassimir D; Kralchevsky, Peter A; Stoyanov, Simeon D; Blijdenstein, Theodorus B J; Arnaudov, Luben N; Pelan, Eddie G; Lips, Alex
2012-06-15
The pendant-drop method (with drop-shape analysis) and Langmuir trough are applied to investigate the characteristic relaxation times and elasticity of interfacial layers from the protein HFBII hydrophobin. Such layers undergo a transition from fluid to elastic solid films. The transition is detected as an increase in the error of the fit of the pendant-drop profile by means of the Laplace equation of capillarity. The relaxation of surface tension after interfacial expansion follows an exponential-decay law, which indicates adsorption kinetics under barrier control. The experimental data for the relaxation time suggest that the adsorption rate is determined by the balance of two opposing factors: (i) the barrier to detachment of protein molecules from bulk aggregates and (ii) the attraction of the detached molecules by the adsorption layer due to the hydrophobic surface force. The hydrophobic attraction can explain why a greater surface coverage leads to a faster adsorption. The relaxation of surface tension after interfacial compression follows a different, square-root law. Such behavior can be attributed to surface diffusion of adsorbed protein molecules that are condensing at the periphery of interfacial protein aggregates. The surface dilatational elasticity, E, is determined in experiments on quick expansion or compression of the interfacial protein layers. At lower surface pressures (<11 mN/m) the experiments on expansion, compression and oscillations give close values of E that are increasing with the rise of surface pressure. At higher surface pressures, E exhibits the opposite tendency and the data are scattered. The latter behavior can be explained with a two-dimensional condensation of adsorbed protein molecules at the higher surface pressures. The results could be important for the understanding and control of dynamic processes in foams and emulsions stabilized by hydrophobins, as well as for the modification of solid surfaces by adsorption of such
Random Matrix Theory in molecular dynamics analysis.
Palese, Luigi Leonardo
2015-01-01
It is well known that, in some situations, principal component analysis (PCA) carried out on molecular dynamics data results in the appearance of cosine-shaped low index projections. Because this is reminiscent of the results obtained by performing PCA on a multidimensional Brownian dynamics, it has been suggested that short-time protein dynamics is essentially nothing more than a noisy signal. Here we use Random Matrix Theory to analyze a series of short-time molecular dynamics experiments which are specifically designed to be simulations with high cosine content. We use as a model system the protein apoCox17, a mitochondrial copper chaperone. Spectral analysis on correlation matrices allows to easily differentiate random correlations, simply deriving from the finite length of the process, from non-random signals reflecting the intrinsic system properties. Our results clearly show that protein dynamics is not really Brownian also in presence of the cosine-shaped low index projections on principal axes.
Exciton dynamics in molecular aggregates
Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A
2006-01-01
The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the characteri
Exciton dynamics in molecular aggregates
Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A
2006-01-01
The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.
Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F
2008-02-01
We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.
Yemloul, Mehdi; Steiner, Emilie; Robert, Anthony; Bouguet-Bonnet, Sabine; Allix, Florent; Jamart-Grégoire, Brigitte; Canet, Daniel
2011-03-24
An organogelation process depends on the gelator-solvent pair. This study deals with the solvent dynamics once the gelation process is completed. The first approach used is relaxometry, i.e., the measurement of toluene proton longitudinal relaxation time T(1) as a function of the proton NMR resonance frequency (here in the 5 kHz to 400 MHz range). Pure toluene exhibits an unexpected T(1) variation, which has been identified as paramagnetic relaxation resulting from an interaction of toluene with dissolved oxygen. In the gel phase, this contribution is retrieved with, in addition, a strong decay at low frequencies assigned to toluene molecules within the gel fibers. Comparison of dispersion curves of pure toluene and toluene in the gel phase leads to an estimate of the proportion of toluene embedded within the organogel (found around 40%). The second approach is based on carbon-13 T(1) and nuclear Overhauser effect measurements, the combination of these two parameters providing direct information about the reorientation of C-H bonds. It appears clearly that reorientation of toluene is the same in pure liquid and in the gel phase. The only noticeable changes in carbon-13 longitudinal relaxation times are due to the so-called chemical shift anisotropy (csa) mechanism and reflect slight modifications of the toluene electronic distribution in the gel phase. NMR diffusion measurements by the pulse gradient spin-echo (PGSE) method allow us to determine the diffusion coefficient of toluene inside the organogel. It is roughly two-thirds of the one in pure toluene, thus indicating that self-diffusion is the only dynamical parameter to be slightly affected when the solvent is inside the gel structure. The whole set of experimental observations leads to the conclusion that, once the gel is formed, the solvent becomes essentially passive, although an important fraction is located within the gel structure.
Zhu, Tianqi; Dos Reis, Mario; Yang, Ziheng
2015-03-01
Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way
Riviere, J. V.; Shokouhi, P.; Marone, C.; Elsworth, D.; Guyer, R. A.; Johnson, P. A.
2015-12-01
We study nonlinear elastic/acoustic phenomena in rocks at the laboratory scale, with the goal of understanding observations at crustal scales, for instance during strong ground motion and earthquake slip processes. In particular, a long-term goal is to relate microstructure of rocks/gouge to nonlinear acoustic properties. A dynamic perturbation with modest (i.e. acoustic) strain amplitude (10-6 Berea sandstone to explore short-term relaxation, down to 10-4s (DAE is the dynamic equivalent of measuring acoustic velocity as a function of applied pressure). We find that early recovery does not follow a logarithmic law, while some earlier studies based on resonance techniques and at times larger than 1s do exhibit log(t)-recovery. From this non-log(t) dataset, we extract a spectrum of relaxation rates and discuss the potential relation between characteristic rates and rock microstructure. We also discuss the possible links between transient elastic softening and transient increase in permeability due to dynamic perturbation.
Salloum, Ahmed
Constraint relaxation by definition means that certain security, operational, or financial constraints are allowed to be violated in the energy market model for a predetermined penalty price. System operators utilize this mechanism in an effort to impose a price-cap on shadow prices throughout the market. In addition, constraint relaxations can serve as corrective approximations that help in reducing the occurrence of infeasible or extreme solutions in the day-ahead markets. This work aims to capture the impact constraint relaxations have on system operational security. Moreover, this analysis also provides a better understanding of the correlation between DC market models and AC real-time systems and analyzes how relaxations in market models propagate to real-time systems. This information can be used not only to assess the criticality of constraint relaxations, but also as a basis for determining penalty prices more accurately. Constraint relaxations practice was replicated in this work using a test case and a real-life large-scale system, while capturing both energy market aspects and AC real-time system performance. System performance investigation included static and dynamic security analysis for base-case and post-contingency operating conditions. PJM peak hour loads were dynamically modeled in order to capture delayed voltage recovery and sustained depressed voltage profiles as a result of reactive power deficiency caused by constraint relaxations. Moreover, impacts of constraint relaxations on operational system security were investigated when risk based penalty prices are used. Transmission lines in the PJM system were categorized according to their risk index and each category was as-signed a different penalty price accordingly in order to avoid real-time overloads on high risk lines. This work also extends the investigation of constraint relaxations to post-contingency relaxations, where emergency limits are allowed to be relaxed in energy market models
Electron spin coherence and effect of spin polarization on electron relaxation dynamics in GaAs
Teng, Lihua; Wang, Xia; Ge, Weikun; Lai, Tianshu
2011-09-01
Time-resolved circularly and linearly polarized pump-probe spectroscopy is used to study the evolution of the electron spin coherence and electron relaxation dynamics in bulk GaAs at 9.6 K. In particular, their dependence on photon energy (or electron excess energy) is carefully investigated. The absorption quantum beats which are observed in circularly polarized pump-probe spectroscopy are obtained, reflecting the dephasing of the electron spin coherence. A circularly dichromatic pump-probe model is developed with both the spin-polarization-dependent band-filling and band-gap renormalization effects being taken into account. The model is used to simulate the differential transmission spectra for the collinearly polarized, co-helicity circularly polarized and cross-helicity circularly polarized pump-probe configurations, respectively. It is found that the model simulates well the features of the absorption quantum beats for a spin-dependent thermalized distribution of the photocreated carriers by a circularly polarized pump pulse, such as the variation of the oscillatory amplitude and phase reversal of the absorption quantum beats with photon energy increase. The simulation is in good agreement with our experimental results and reveals the effect of spin polarization on electron relaxation dynamics.
Femtosecond spectroscopy study of the exciton relaxation dynamics in silicon quantum dots
Kryschi, Carola; Kuntermann, Volker; Cimpean, Carla [Institut fuer Physikalische Chemie I, FAU, Erlangen (Germany); Haarer, Dietrich [BIMF, Universitaet Bayreuth (Germany)
2008-07-01
This contribution is targeted to the development of surface-modified silicon quantum dots (Siqdots) with tailored luminescence properties. The surface modification of Siqdots with sizes between 1 and 5 nm has been successfully achieved via two different synthesis routes, first, by controlled oxidation followed from silanization and second, by thermal hydrosilylation with chromophores. The luminescence properties of ethanolic Siqdots dispersions were characterized using stationary and time-resolved luminescence spectroscopy techniques, whereas the ultrashort exciton relaxation dynamics were examined using femtosecond transient absorption spectroscopy. Silanized Siqdots were observed to exhibit two species of photoluminescence (PL): the blue emission at 380 nm is assigned to localized surface states, whereas radiative recombination of quantum confined excitons gives rise to a broad PL band around 800 nm. Whereas the latter is ascribed to Siqdots with sizes larger than 3 nm, for Siqdots smaller than 1.5 nm exciton relaxation dynamics is understood to occur predominantly by trapping due to lower-lying surface states which may radiatively decay. Siqdots terminated with suited chromophores were observed to exhibit only one PL band in the visible that is ascribed to exciton states involving resonant couplings to the conjugated electron system of the chromophores.
Barrientos, Eva; Pelayo, Fernández; Tanaka, Eiji; Lamela-Rey, María Jesús; Fernández-Canteli, Alfonso
2016-04-01
In this study, the dynamic and static compressive properties of the whole porcine temporomandibular joint (TMJ) disc were investigated. The aim of the study was to develop a new simple method for the evaluation of joint viscoelasticity, enabling examination of the load-bearing capacity and joint flexibility of the entire disc. For the experiments, a novel testing fixture that reproduces the condylar and fossa surfaces of the TMJ was developed to replicate TMJ disc geometry. Ten porcine discs were used in the experiments. Each disc was dissected from the TMJ and sinusoidal compressive strain was applied to obtain the storage and loss moduli. Static strain control tests were carried out to obtain the relaxation modulus. The result of static and dynamic tests indicated that the whole disc presented viscoelastic behavior under compression. Storage and loss moduli increased with frequency and the relaxation modulus decreased over time. The loss tangent showed less frequency dependence, with values ranging from 0.2 to 0.3, suggesting that the viscous properties of the disc cannot be neglected. These results provide a better understanding of whole disc mechanical compression behavior under realistic TMJ working conditions.
Active site dynamics in NADH oxidase from Thermus thermophilus studied by NMR spin relaxation.
Miletti, Teresa; Farber, Patrick J; Mittermaier, Anthony
2011-09-01
We have characterized the backbone dynamics of NADH oxidase from Thermus thermophilus (NOX) using a recently-developed suite of NMR experiments designed to isolate exchange broadening, together with (15)N R (1), R (1ρ ), and {(1)H}-(15)N steady-state NOE relaxation measurements performed at 11.7 and 18.8 T. NOX is a 54 kDa homodimeric enzyme that belongs to a family of structurally homologous flavin reductases and nitroreductases with many potential biotechnology applications. Prior studies have suggested that flexibility is involved in the catalytic mechanism of the enzyme. The active site residue W47 was previously identified as being particularly important, as its level of solvent exposure correlates with enzyme activity, and it was observed to undergo "gating" motions in computer simulations. The NMR data are consistent with these findings. Signals from W47 are dynamically broadened beyond detection and several other residues in the active site have significant R ( ex ) contributions to transverse relaxation rates. In addition, the backbone of S193, whose side chain hydroxyl proton hydrogen bonds directly with the FMN cofactor, exhibits extensive mobility on the ns-ps timescale. We hypothesize that these motions may facilitate structural rearrangements of the active site that allow NOX to accept both FMN and FAD as cofactors.
Maldonado-Camargo, L. [Department of Chemical Engineering, University of Florida, Gainesville, FL 32611 (United States); Torres-Díaz, I. [J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611 (United States); Chiu-Lam, A. [Department of Chemical Engineering, University of Florida, Gainesville, FL 32611 (United States); Hernández, M. [J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611 (United States); Rinaldi, C., E-mail: carlos.rinaldi@bme.ufl.edu [Department of Chemical Engineering, University of Florida, Gainesville, FL 32611 (United States); J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611 (United States)
2016-08-15
We demonstrate how dynamic magnetic susceptibility measurements (DMS) can be used to estimate the relative contributions of Brownian and Néel relaxation to the dynamic magnetic response of a magnetic fluid, a suspension of magnetic nanoparticles. The method applies to suspensions with particles that respond through Brownian or Néel relaxation and for which the characteristic Brownian and Néel relaxation times are widely separated. First, we illustrate this using magnetic fluids consisting of mixtures of particles that relax solely by the Brownian or Néel mechanisms. Then, it is shown how the same approach can be applied to estimate the relative contributions of Brownian and Néel relaxation in a suspension consisting of particles obtained from a single synthesis and whose size distribution straddles the transition from Néel to Brownian relaxation. - Highlights: • Method to estimate the contributions of the relaxation mechanism to the magnetic response. • Method applies to cases where the Brownian and Néel peaks do not overlap. • The method applies for ferrofluids prepared with as–synthesized particles.
Liouville-von Neumann molecular dynamics
Jakowski, Jacek; Morokuma, Keiji
2009-06-01
We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.
Lamley, Jonathan M; Lougher, Matthew J; Sass, Hans Juergen; Rogowski, Marco; Grzesiek, Stephan; Lewandowski, Józef R
2015-09-14
Typically, protein dynamics involve a complex hierarchy of motions occurring on different time scales between conformations separated by a range of different energy barriers. NMR relaxation can in principle provide a site-specific picture of both the time scales and amplitudes of these motions, but independent relaxation rates sensitive to fluctuations in different time scale ranges are required to obtain a faithful representation of the underlying dynamic complexity. This is especially pertinent for relaxation measurements in the solid state, which report on dynamics in a broader window of time scales by more than 3 orders of magnitudes compared to solution NMR relaxation. To aid in unraveling the intricacies of biomolecular dynamics we introduce (13)C spin-lattice relaxation in the rotating frame (R1ρ) as a probe of backbone nanosecond-microsecond motions in proteins in the solid state. We present measurements of (13)C'R1ρ rates in fully protonated crystalline protein GB1 at 600 and 850 MHz (1)H Larmor frequencies and compare them to (13)C'R1, (15)N R1 and R1ρ measured under the same conditions. The addition of carbon relaxation data to the model free analysis of nitrogen relaxation data leads to greatly improved characterization of time scales of protein backbone motions, minimizing the occurrence of fitting artifacts that may be present when (15)N data is used alone. We also discuss how internal motions characterized by different time scales contribute to (15)N and (13)C relaxation rates in the solid state and solution state, leading to fundamental differences between them, as well as phenomena such as underestimation of picosecond-range motions in the solid state and nanosecond-range motions in solution.
Advances in molecular vibrations and collision dynamics molecular clusters
Bacic, Zatko
1998-01-01
This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...
Ab initio Molecular Dynamics Study on Small Carbon Nanotubes
叶林晖; 刘邦贵; 王鼎盛
2001-01-01
Ab initio molecular dynamics simulations are performed on small single wall nanotubes. By structural relaxation,the equilibrium C-C bond lengths and bond angles are determined. Our result shows that for both zigzag and armchair nanotubes there are two nonequivalent bond lengths. One bond stretches from that of the graphene sheet, while the other shrinks. Small variations on bond angles are also shown. Energy bands are calculated for the optimized structures. It is found that the intrinsic curvature of the very small nanotube greatly modifies the energy band which can no longer be well described in the tight-binding zone-folding picture. In our calculation very small nanotubes are metallic. The energy per atom fits quite well with the relation of E(R) = E0 + f/R2 even for the extreme small radius. The implications of the results on the properties of small nanotubes are discussed.
Scalable Molecular Dynamics for Large Biomolecular Systems
Robert K. Brunner
2000-01-01
Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.
Theory and application of quantum molecular dynamics
Zeng Hui Zhang, John
1999-01-01
This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli
Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers
2017-01-01
Conspectus Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition
Molecular Biodynamers: Dynamic Covalent Analogues of Biopolymers.
Liu, Yun; Lehn, Jean-Marie; Hirsch, Anna K H
2017-02-21
Constitutional dynamic chemistry (CDC) features the use of reversible linkages at both molecular and supramolecular levels, including reversible covalent bonds (dynamic covalent chemistry, DCC) and noncovalent interactions (dynamic noncovalent chemistry, DNCC). Due to its inherent reversibility and stimuli-responsiveness, CDC has been widely utilized as a powerful tool for the screening of bioactive compounds, the exploitation of receptors or substrates driven by molecular recognition, and the fabrication of constitutionally dynamic materials. Implementation of CDC in biopolymer science leads to the generation of constitutionally dynamic analogues of biopolymers, biodynamers, at the molecular level (molecular biodynamers) through DCC or at the supramolecular level (supramolecular biodynamers) via DNCC. Therefore, biodynamers are prepared by reversible covalent polymerization or noncovalent polyassociation of biorelevant monomers. In particular, molecular biodynamers, biodynamers of the covalent type whose monomeric units are connected by reversible covalent bonds, are generated by reversible polymerization of bio-based monomers and can be seen as a combination of biopolymers with DCC. Owing to the reversible covalent bonds used in DCC, molecular biodynamers can undergo continuous and spontaneous constitutional modifications via incorporation/decorporation and exchange of biorelevant monomers in response to internal or external stimuli. As a result, they behave as adaptive materials with novel properties, such as self-healing, stimuli-responsiveness, and tunable mechanical and optical character. More specifically, molecular biodynamers combine the biorelevant characters (e.g., biocompatibility, biodegradability, biofunctionality) of bioactive monomers with the dynamic features of reversible covalent bonds (e.g., changeable, tunable, controllable, self-healing, and stimuli-responsive capacities), to realize synergistic properties in one system. In addition, molecular
Molecular dynamics model of dimethyl ether
Lin, B.; Halley, W.J. [Univ. of Minnesota, Minneapolis, MN (United States)
1995-11-02
We report a molecular dynamics model of the monomeric liquid dimethyl ether. The united atom approach is used to treat CH{sub 3} groups as point source centers. Partial charges are derived from the experimental dipole moment. Harmonic force constants are used for intramolecular interactions, and their values are so chosen that the model`s fundamental frequencies agree with experimental results. Because we are interested in solvation properties, the model contains flexible molecules, allowing molecular distortion and internal dynamical quantities. We report radial distribution functions and the static structure factors as well as some dynamical quantities such as the dynamical structure factor, infrared absorption, and Raman scattering spectra. Calculated results agree reasonably well with experimental and other simulation results. 25 refs., 8 figs., 1 tab.
Molecular dynamic simulations of ocular tablet dissolution.
Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire
2013-11-25
Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies.
Magnetocaloric effect in Mn2-pyrazole-[Nb(CN)8] molecular magnet by relaxation calorimetry
Pełka, R.; Gajewski, M.; Miyazaki, Y.; Yamashita, S.; Nakazawa, Y.; Fitta, M.; Pinkowicz, D.; Sieklucka, B.
2016-12-01
Magnetocaloric effect in {[Mn(pyrazole)4]2[Nb(CN)8]·4 H2O}n molecular magnet is reported. It crystallizes in tetragonal I41/a space group. The compound exhibits a phase transition to a long range magnetically ordered state at TN ≈ 22.8 K. Temperature dependences of the magnetic entropy change ΔSM as well as the adiabatic temperature change ΔTad due to applied field change μ0 ΔH in the range of 0.1-9 T have been inferred from the relaxation calorimetry measurements. A systematic approximate approach has been used to determine the lattice contribution to the heat capacity. The maximum value of ΔSM for μ0 ΔH = 5 T is 6.83 J mol-1 K-1 (6.65 J kg-1 K-1) at 24.3 K. The corresponding maximum value of ΔTad is 1.4 K at 23.8 K. The temperature dependence of the exponent n characterizing the field dependence of ΔSM has been estimated. It attains the value of 0.64 at the transition temperature, which is consistent with the 3D Heisenberg universality class. A hitherto unobserved two-peak structure has been revealed in the temperature dependence of ΔTad.
Relaxed molecular clock provides evidence for long-distance dispersal of Nothofagus (southern beech.
Michael Knapp
2005-01-01
Full Text Available Nothofagus (southern beech, with an 80-million-year-old fossil record, has become iconic as a plant genus whose ancient Gondwanan relationships reach back into the Cretaceous era. Closely associated with Wegener's theory of "Kontinentaldrift", Nothofagus has been regarded as the "key genus in plant biogeography". This paradigm has the New Zealand species as passengers on a Moa's Ark that rafted away from other landmasses following the breakup of Gondwana. An alternative explanation for the current transoceanic distribution of species seems almost inconceivable given that Nothofagus seeds are generally thought to be poorly suited for dispersal across large distances or oceans. Here we test the Moa's Ark hypothesis using relaxed molecular clock methods in the analysis of a 7.2-kb fragment of the chloroplast genome. Our analyses provide the first unequivocal molecular clock evidence that, whilst some Nothofagus transoceanic distributions are consistent with vicariance, trans-Tasman Sea distributions can only be explained by long-distance dispersal. Thus, our analyses support the interpretation of an absence of Lophozonia and Fuscospora pollen types in the New Zealand Cretaceous fossil record as evidence for Tertiary dispersals of Nothofagus to New Zealand. Our findings contradict those from recent cladistic analyses of biogeographic data that have concluded transoceanic Nothofagus distributions can only be explained by vicariance events and subsequent extinction. They indicate that the biogeographic history of Nothofagus is more complex than envisaged under opposing polarised views expressed in the ongoing controversy over the relevance of dispersal and vicariance for explaining plant biodiversity. They provide motivation and justification for developing more complex hypotheses that seek to explain the origins of Southern Hemisphere biota.
Neutron Star Crust and Molecular Dynamics Simulation
Horowitz, C J; Schneider, A; Berry, D K
2011-01-01
In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.
Lazutin, A. A.; Glagolev, M. K.; Vasilevskaya, V. V.; Khokhlov, A. R. [A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova Str. 28, 119991 Moscow (Russian Federation)
2014-04-07
An algorithm involving classical molecular dynamics simulations with mapping and reverse mapping procedure is here suggested to simulate the crosslinking of the polystyrene dissolved in dichloroethane by monochlorodimethyl ether. The algorithm comprises consecutive stages: molecular dynamics atomistic simulation of a polystyrene solution, the mapping of atomistic structure onto coarse-grained model, the crosslink formation, the reverse mapping, and finally relaxation of the structure dissolved in dichloroethane and in dry state. The calculated values of the specific volume and the elastic modulus are in reasonable quantitative correspondence with experimental data.
Molecular Dynamics Simulations of Network Glasses
Drabold, David A.
The following sections are included: * Introduction and Background * History and use of MD * The role of the potential * Scope of the method * Use of a priori information * Appraising a model * MD Method * Equations of motion * Energy minimization and equilibration * Deeper or global minima * Simulated annealing * Genetic algorithms * Activation-relaxation technique * Alternate dynamics * Modeling infinite systems: Periodic boundary conditions * The Interatomic Interactions * Overview * Empirical classical potentials * Potentials from electronic structure * The tight-binding method * Approximate methods based on tight-binding * First principles * Local basis: "ab initio tight binding" * Plane-waves: Car-Parrinello methods * Efficient ab initio methods for large systems * The need for locality of electron states in real space * Avoiding explicit orthogonalization * Connecting Simulation to Experiment * Structure * Network dynamics * Computing the harmonic modes * Dynamical autocorrelation functions * Dynamical structure factor * Electronic structure * Density of states * Thermal modulation of the electron states * Transport * Applications * g-GeSe2 * g-GexSe1-x glasses * Amorphous carbon surface * Where to Get Codes to Get Started * Acknowledgments * References
Microscopic origins of the terahertz carrier relaxation and cooling dynamics in graphene
Mihnev, Momchil T.; Kadi, Faris; Divin, Charles J.; Winzer, Torben; Lee, Seunghyun; Liu, Che-Hung; Zhong, Zhaohui; Berger, Claire; de Heer, Walt A.; Malic, Ermin; Knorr, Andreas; Norris, Theodore B.
2016-01-01
The ultrafast dynamics of hot carriers in graphene are key to both understanding of fundamental carrier–carrier interactions and carrier–phonon relaxation processes in two-dimensional materials, and understanding of the physics underlying novel high-speed electronic and optoelectronic devices. Many recent experiments on hot carriers using terahertz spectroscopy and related techniques have interpreted the variety of observed signals within phenomenological frameworks, and sometimes invoke extrinsic effects such as disorder. Here, we present an integrated experimental and theoretical programme, using ultrafast time-resolved terahertz spectroscopy combined with microscopic modelling, to systematically investigate the hot-carrier dynamics in a wide array of graphene samples having varying amounts of disorder and with either high or low doping levels. The theory reproduces the observed dynamics quantitatively without the need to invoke any fitting parameters, phenomenological models or extrinsic effects such as disorder. We demonstrate that the dynamics are dominated by the combined effect of efficient carrier–carrier scattering, which maintains a thermalized carrier distribution, and carrier–optical–phonon scattering, which removes energy from the carrier liquid. PMID:27221060
Thermodynamic scaling of molecular dynamics in supercooled ibuprofen.
Adrjanowicz, K; Wojnarowska, Z; Paluch, M; Pionteck, J
2011-04-28
It was shown recently that ibuprofen revealed a strong tendency to form hydrogen bonded aggregates such as dimers and trimers of either cyclic or linear geometry, which somehow seems to control molecular mobility of that drug [Brás et al. J. Phys. Chem. B2008, 112 (35), 11 087-11 099]. For such hydrogen-bonded liquids, superpositioning of dynamics under various temperature T, pressure P, and volume V conditions, when plotted versus the scaling function of T(-1)V(-γ) (where γ is a material constant), may not always be satisfying. In the present work, we have tested the validity of this scaling for supercooled ibuprofen. In order to do that, pressure-volume-temperature (PVT) measurements combined with isobaric and isothermal dielectric relaxation studies (pressure up to 310 MPa) were carried out. The scaling properties of the examined drug were derived from the fitting of the τ(α)(T,V) dependences to the modified Avramov equation and by analyzing in double logarithmic scale the T(g)(V(g)) dependences, where the glass transition temperature T(g) and volume V(g) were defined for various relaxation times. In view of the obtained results, we conjecture that for ibuprofen the thermodynamic scaling idea works but not perfectly. The slight departure from the scaling behavior is discussed in the context of the hydrogen bonding abilities of the examined system and compared with the results reported for other strongly associated liquids.
Molecular dynamics simulation of impact test
Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt
1998-11-01
This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)
Reaction dynamics in polyatomic molecular systems
Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.
Molecular dynamics modeling of structural battery components
Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.
2015-01-01
A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion compo
Catalysis and communication in dynamic molecular networks
Fanlo Virgos, Hugo
2015-01-01
The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity
Dynamical Relaxation of Coronal Magnetic Fields. III. 3D Spiral Nulls
Fuentes-Fernandez, Jorge
2012-01-01
Context: The majority of studies on stressed 3D magnetic null points consider magnetic reconnection driven by an external perturbation, but the formation of a genuine current sheet equilibrium remains poorly understood. This problem has been considered more extensively in two-dimensions, but lacks a generalization into 3D fields. Aims: 3D magnetic nulls are more complex than 2D nulls and the field can take a greater range of magnetic geometries local to the null. Here, we focus on one type and consider the dynamical non-resistive relaxation of 3D spiral nulls with initial spine-aligned current. We aim to provide a valid magnetohydrostatic equilibrium, and describe the electric current accumulations in various cases, involving a finite plasma pressure. Methods: A full MHD code is used, with the resistivity set to zero so that reconnection is not allowed, to run a series of experiments in which a perturbed spiral 3D null point is allowed to relax towards an equilibrium, via real, viscous damping forces. Changes...
Nicolas Garraud
2017-05-01
Full Text Available The design and validation of a magnetic particle spectrometer (MPS system used to study the linear and nonlinear behavior of magnetic nanoparticle suspensions is presented. The MPS characterizes the suspension dynamic response, both due to relaxation and saturation effects, which depends on the magnetic particles and their environment. The system applies sinusoidal excitation magnetic fields varying in amplitude and frequency and can be configured for linear measurements (1 mT at up to 120 kHz and nonlinear measurements (50 mT at up to 24 kHz. Time-resolved data acquisition at up to 4 MS/s combined with hardware and software-based signal processing allows for wide-band measurements up to 50 harmonics in nonlinear mode. By cross-calibrating the instrument with a known sample, the instantaneous sample magnetization can be quantitatively reconstructed. Validation of the two MPS modes are performed for iron oxide and cobalt ferrite suspensions, exhibiting Néel and Brownian relaxation, respectively.
Mondal, Ritwik; Berritta, Marco; Oppeneer, Peter M.
2016-10-01
Starting from the Dirac-Kohn-Sham equation, we derive the relativistic equation of motion of spin angular momentum in a magnetic solid under an external electromagnetic field. This equation of motion can be rewritten in the form of the well-known Landau-Lifshitz-Gilbert equation for a harmonic external magnetic field and leads to a more general magnetization dynamics equation for a general time-dependent magnetic field. In both cases there is an electronic spin-relaxation term which stems from the spin-orbit interaction. We thus rigorously derive, from fundamental principles, a general expression for the anisotropic damping tensor which is shown to contain an isotropic Gilbert contribution as well as an anisotropic Ising-like and a chiral, Dzyaloshinskii-Moriya-like contribution. The expression for the spin relaxation tensor comprises furthermore both electronic interband and intraband transitions. We also show that when the externally applied electromagnetic field possesses spin angular momentum, this will lead to an optical spin torque exerted on the spin moment.
Ultrafast charge generation and relaxation dynamics in methylammonium lead bromide perovskites
Deng, Xiaofan; Wen, Xiaoming; Sheng, Rui; Huang, Shujuan; Harada, Takaaki; Kee, Tak W.; Green, Martin A.; Ho-Baillie, Anita
2015-12-01
Methylammonium Lead Bromide (CH3NH3PbBr3) is a promising material for tandem solar cell due to its high band gap. Ultrafast optical techniques on a time scale of femto- and picosecond are used to investigate the carrier dynamics in CH3NH3PbBr3. An ultrafast cooling of hot carriers occurs in sub-picoseconds in CH3NH3PbBr3 by phonon scattering. Two ultrafast relaxation processes are attributed to optical phonon scattering and acoustic phonon scattering. The relaxation processes are evidently slower when CH3NH3PbBr3 is in contact with compact TiO2 (c-TiO2) layer, suggesting better quality CH3NH3PbBr3. when deposited on c-TiO2. The nanosecond decay in CH3NH3PbBr3 film is ascribed to electron-hole recombination. With the presence of c-TiO2 layer, this process is accelerated due to electron transport across the CH3NH3PbBr3/ c-TiO2 interface.
Direct 13C-detection for carbonyl relaxation studies of protein dynamics
Pasat, Gabriela; Zintsmaster, John S.; Peng, Jeffrey W.
2008-08-01
We describe a method that uses direct 13C-detection for measuring rotating-frame carbonyl ( 13CO) relaxation rates to describe protein functional dynamics. Key advantages of method include the following: (i) unique access to 13CO groups that lack a scalar-coupled 15N- 1H group; (ii) insensitivity to 15N/ 1H exchange-broadening that can derail 1H-detected 15N and HNCO methods; (iii) avoidance of artifacts caused by incomplete water suppression. We demonstrate the approach for both backbone and side-chain 13CO groups. Accuracy of the 13C-detected results is supported by their agreement with those obtained from established HNCO-based approaches. Critically, we show that the 13C-detection approach provides access to the 13CO groups of functionally important residues that are invisible via 1H-detected HNCO methods because of exchange-broadening. Hence, the 13C-based method fills gaps inherent in canonical 1H-detected relaxation experiments, and thus provides a novel complementary tool for NMR studies of biomolecular flexibility.
Kirtil, Emrah; Dag, Damla; Guner, Selen; Unal, Kubra; Oztop, Mecit H
2017-09-01
Liposomes are lipid bilayer vesicles that can be used as encapsulation systems for bioactive agents to provide increased protection against environmental stresses (such as pH or temperature extremes). Time Domain Nuclear Magnetic Resonance (TD-NMR) that is based on differentiation of specimen contents with respect to magnetic relaxation rates provides detailed information on amount, state and distribution of water and oil and provide reproducible results on the samples. These make TD-NMR particularly suitable for time-dependent monitoring of emulsion system dynamics. In this study, spin-spin (T2) relaxation times and relaxation spectra were used for characterizing green tea extract loaded and unloaded liposomes prepared with soy (S75) and egg lecithins (E80) by different preparation methods (such as homogenization type, pressure and solvent type). Mean particle sizes of liposomes were found to be the most influential factor in shaping mono-exponential T2 relaxation times. The differences in particle sizes of E80 and S75 samples along with samples with different homogenization pressures could be monitored with T2 relaxation times. Additionally, T2 relaxation times were found to be correlated with particle shape irregularity, and chemical instability of samples due to lipid oxidation. With relaxation spectrum analysis, particular components in the sample could be distinguished (internal/external water and lipid bilayers), which gave more elaborate results on mechanisms of instability. Copyright © 2017 Elsevier Ltd. All rights reserved.
Multiscale coupling of molecular dynamics and peridynamics
Tong, Qi; Li, Shaofan
2016-10-01
We propose a multiscale computational model to couple molecular dynamics and peridynamics. The multiscale coupling model is based on a previously developed multiscale micromorphic molecular dynamics (MMMD) theory, which has three dynamics equations at three different scales, namely, microscale, mesoscale, and macroscale. In the proposed multiscale coupling approach, we divide the simulation domain into atomistic region and macroscale region. Molecular dynamics is used to simulate atom motions in atomistic region, and peridynamics is used to simulate macroscale material point motions in macroscale region, and both methods are nonlocal particle methods. A transition zone is introduced as a messenger to pass the information between the two regions or scales. We employ the "supercell" developed in the MMMD theory as the transition element, which is named as the adaptive multiscale element due to its ability of passing information from different scales, because the adaptive multiscale element can realize both top-down and bottom-up communications. We introduce the Cauchy-Born rule based stress evaluation into state-based peridynamics formulation to formulate atomistic-enriched constitutive relations. To mitigate the issue of wave reflection on the interface, a filter is constructed by switching on and off the MMMD dynamic equations at different scales. Benchmark tests of one-dimensional (1-D) and two-dimensional (2-D) wave propagations from atomistic region to macro region are presented. The mechanical wave can transit through the interface smoothly without spurious wave deflections, and the filtering process is proven to be efficient.
Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann
Melenev, Petr
2017-06-01
Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces.
Molecular Dynamics Study of Polyethylene under Extreme Confinement
Kritikos, G.; Sgouros, A.; Vogiatzis, G. G.; Theodorou, D. N.
2016-08-01
We present results concerning the dynamics and the structure of adsorbed layers of molten polyethylene (PE) between two graphite surfaces. The molecular weight of the monodisperse PE chains reaches the entanglement regime. We study three cases of interwall distances, equal to two, three and four times the unperturbed radius of gyration (Rg ) of PE chains. The confined system is equilibrated by use of efficient Monte Carlo (MC) algorithms. Conducting molecular dynamics (MD) simulations, we reveal the distribution of relaxation times as a function of distance from the graphite walls at the temperature of 450 K. From the atomic-level stresses we calculate a realistic estimate of the adhesion tension, which is not affected significantly by the width of the pore. Although the distance between the two walls is comparable to the width of the adsorbed layer, we do not record the formation of ‘glassy bridges’ under the studied conditions. The diffusion of polymer chains in the middle layer is not inhibited by the existence of the two adsorbed layers. Extreme confinement conditions imposed by the long range wall potentials bring about an increase in both the adsorption and desorption rates of chains. The presented results seem to cohere with a reduction in the calorimetric (heat capacity step) glass transition temperature (Tg ).
MDMovie: a molecular dynamics viewing tool.
Greenberg, J P
1996-10-01
The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.
Extensional Relaxation Times and Pinch-off Dynamics of Dilute Polymer Solutions
Dinic, Jelena; Zhang, Yiran; Jimenez, Leidy; Sharma, Vivek
2015-11-01
We show that visualization and analysis of capillary-driven thinning and pinch-off dynamics of the columnar neck in an asymmetric liquid bridge created by dripping-onto-substrate can be used for characterizing the extensional rheology of complex fluids. Using a particular example of dilute, aqueous PEO solutions, we show the measurement of both the extensional relaxation time and extensional viscosity of weakly elastic, polymeric complex fluids with low shear viscosity ηsessile drop to a nozzle is detected optically, and the extensional response for viscoelastic fluids is characterized by analyzing their elastocapillary self-thinning, we refer to this technique as optically-detected elastocapillary self-thinning dripping-onto-substrate (ODES-DOS) extensional rheometry.
Coupling dynamics of Nb/Nb2O5 relaxation oscillators.
Li, Shuai; Liu, Xinjun; Nandi, Sanjoy Kumar; Venkatachalam, Dinesh Kumar; Elliman, Robert Glen
2017-03-24
The coupling dynamics of capacitively coupled Nb/Nb2O5 relaxation oscillators are shown to exhibit rich collective behaviour depending on the negative differential resistance response of the individual devices, the operating voltage and the coupling capacitance. These coupled oscillators are shown to exhibit stable frequency and phase locking states at source voltages as low as 2.2 V, with frequency control in the range from 0.85 to 16.2 MHz and frequency tunability of ∼8 MHz V(-1). The experimental realisation of such compact, scalable and low power coupled-oscillator systems is of particular significance for the development and implementation of large oscillator networks in non-Boolean computing architectures.
Ultrafast photo-induced turning of magnetization and its relaxation dynamics in GaMnAs
无
2010-01-01
We report that,by linearly polarized pumping of different wavelengths,Kerr transients appear at zero magnetic field only in the case when GaMnAs samples are initialized at 3 K by first applying a 0.8 Tesla field and then returning to zero field.We find that,instead of magnetization precession,the near-band gap excitation induces a coherent out-of-plane turning of magnetization,which shows very long relaxation dynamics with no precession.When photon energy increases,the peak value of the Kerr transient increases,but it decays rapidly to the original slow transient seen under the near-band-gap excitation.
Dipolar Relaxation Dynamics at the Active Site of an ATPase Regulated by Membrane Lateral Pressure.
Fischermeier, Elisabeth; Pospíšil, Petr; Sayed, Ahmed; Hof, Martin; Solioz, Marc; Fahmy, Karim
2017-01-24
The active transport of ions across biological membranes requires their hydration shell to interact with the interior of membrane proteins. However, the influence of the external lipid phase on internal dielectric dynamics is hard to access by experiment. Using the octahelical transmembrane architecture of the copper-transporting P1B -type ATPase from Legionella pneumophila as a model structure, we have established the site-specific labeling of internal cysteines with a polarity-sensitive fluorophore. This enabled dipolar relaxation studies in a solubilized form of the protein and in its lipid-embedded state in nanodiscs. Time-dependent fluorescence shifts revealed the site-specific hydration and dipole mobility around the conserved ion-binding motif. The spatial distribution of both features is shaped significantly and independently of each other by membrane lateral pressure. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Understanding ion association states and molecular dynamics using infrared spectroscopy
Masser, Hanqing
microphase separates from the PEO-rich microphase, and ionic groups are preferentially solvated by PEO chains and reside in the PEO-rich microphase. As the ratio of PTMO increases, the fraction of aggregates increases, resulting in more highly coordinated aggregation states. Results on ion association states are in good agreement with previous results on ion conductivity, polymer dynamics and morphology. The effects of ion content, cation type and ionic side chain structure on ion association states are systemically studied in a series of ionomers with short ethylene oxide and ionic sulfonated styrene side chains, and then correlated to the ion and polymer dynamic characterization. It is found that ionomers with modest ion content, large cation and styrene ionic side chain have the most "free ions" and ion pairs, and highest ion conductivity. Ion conduction in ionomers is optimized by systematically changing their chemical structures. In addition to knowledge of ion association states, a IR band shape also contains information on molecular dynamics. In companion investigation, the vibrational relaxation and dynamic transitions of conformationally insensitive normal modes in two different polymer systems (atactic polystyrene and deuterated poly(methyl methacrylate)) are studied. The information on vibrational relaxations is resolved by conducting precisely controlled FTIR experiments, applying specialized curve resolving data analysis, and calculating time correlation functions through numerical Fourier transformation. The vibrational relaxations of these modes can be described by a two process model: a fast process on the time scale of 0.01 ps, which is inhomogeneously broadened by a slow process on the time scale of picoseconds.
Rangel, David P; Baveye, Philippe C; Robinson, Bruce H
2012-06-07
We simulate spin relaxation processes, which may be measured by either continuous wave or pulsed magnetic resonance techniques, using trajectory-based simulation methodologies. The spin-lattice relaxation rates are extracted numerically from the relaxation simulations. The rates obtained from the numerical fitting of the relaxation curves are compared to those obtained by direct simulation from the relaxation Bloch-Wangsness-Abragam-Redfield theory (BWART). We have restricted our study to anisotropic rigid-body rotational processes, and to the chemical shift anisotropy (CSA) and a single spin-spin dipolar (END) coupling mechanisms. Examples using electron paramagnetic resonance (EPR) nitroxide and nuclear magnetic resonance (NMR) deuterium quadrupolar systems are provided. The objective is to compare those rates obtained by numerical simulations with the rates obtained by BWART. There is excellent agreement between the simulated and BWART rates for a Hamiltonian describing a single spin (an electron) interacting with the bath through the chemical shift anisotropy (CSA) mechanism undergoing anisotropic rotational diffusion. In contrast, when the Hamiltonian contains both the chemical shift anisotropy (CSA) and the spin-spin dipolar (END) mechanisms, the decay rate of a single exponential fit of the simulated spin-lattice relaxation rate is up to a factor of 0.2 smaller than that predicted by BWART. When the relaxation curves are fit to a double exponential, the slow and fast rates extracted from the decay curves bound the BWART prediction. An extended BWART theory, in the literature, includes the need for multiple relaxation rates and indicates that the multiexponential decay is due to the combined effects of direct and cross-relaxation mechanisms.
Molecular dynamics and composition of crude oil by low-field nuclear magnetic resonance.
Jia, Zijian; Xiao, Lizhi; Wang, Zhizhan; Liao, Guangzhi; Zhang, Yan; Liang, Can
2016-08-01
Nuclear magnetic resonance (NMR) techniques are widely used to identify pure substances and probe protein dynamics. Oil is a complex mixture composed of hydrocarbons, which have a wide range of molecular size distribution. Previous work show that empirical correlations of relaxation times and diffusion coefficients were found for simple alkane mixtures, and also the shape of the relaxation and diffusion distribution functions are related to the composition of the fluids. The 2D NMR is a promising qualitative evaluation method for oil composition. But uncertainty in the interpretation of crude oil indicated further study was required. In this research, the effect of each composition on relaxation distribution functions is analyzed in detail. We also suggest a new method for prediction of the rotational correlation time distribution of crude oil molecules using low field NMR (LF-NMR) relaxation time distributions. A set of down-hole NMR fluid analysis system is independently designed and developed for fluid measurement. We illustrate this with relaxation-relaxation correlation experiments and rotational correlation time distributions on a series of hydrocarbon mixtures that employ our laboratory-designed downhole NMR fluid analyzer. The LF-NMR is a useful tool for detecting oil composition and monitoring oil property changes. Copyright © 2016 John Wiley & Sons, Ltd.
Xiaoyan Li; Wei Yang
2005-01-01
A multiple time step algorithm, called reversible reference system propagator algorithm, is introduced for thelong time molecular dynamics simulation. In contrast to the conventional algorithms, the multiple time method has better convergence, stability and efficiency. The method is validated by simulating free relaxation and the hypervelocity impact of nano-clusters. The time efficiency of the multiple time step method enables us to investigate the long time interaction between lattice dislocations and low-angle grain boundaries.
Dynamics and Thermodynamics of Molecular Machines
Golubeva, Natalia
2014-01-01
Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical...... of the important trade-off between power output and efficiency. Steric motor-motor interactions are shown to play an important thermodynamic role by enhancing the EMP as compared to the noninteracting case. Remarkably, the enhancement occurs at biologically relevant parameters. Finally, a generic model of motor...
Dynamical quenching of tunneling in molecular magnets
José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)
2015-12-15
It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.
Sappey, R. E-mail: sappey@physics.ucsd.edu; Vincent, E.; Ocio, M.; Hammann, J
2000-11-01
We discuss here the nature of the low-temperature magnetic relaxation in samples of magnetic nanoparticles. In addition to usual magnetic viscosity measurement, we have used the residual memory ratio (RMR) method. This procedure enables us to overcome the uncertainties usually associated with the energy barrier distribution, thus giving a more detailed insight on the nature of the observed dynamics. A custom-made apparatus coupling dilution refrigeration and SQUID magnetometry allowed measurements of very diluted samples at temperatures ranging between 60 mK and 7 K. Two types of particles have been studied: {gamma}-Fe{sub 2}O{sub 3} of moderate anisotropy, and CoFe{sub 2}O{sub 4} of higher anisotropy where quantum effects are more likely to occur. In both cases, the data cannot simply be interpreted in terms of mere thermally activated dynamics of independent particles. The deviation from thermal activation seems to go opposite of what is expected from the possible effect of particle interactions. We therefore believe that it suggests the occurrence of quantum dynamics at very low temperatures.
Dynamic relaxation in algebraic reconstruction technique (ART) for breast tomosynthesis imaging.
Oliveira, N; Mota, A M; Matela, N; Janeiro, L; Almeida, P
2016-08-01
A major challenge in Digital Breast Tomosynthesis (DBT) is handling image noise since the 3D reconstructed images are obtained from low dose projections and limited angular range. The use of the iterative reconstruction algorithm Algebraic Reconstruction Technique (ART) in clinical context depends on two key factors: the number of iterations needed (time consuming) and the image noise after iterations. Both factors depend highly on a relaxation coefficient (λ), which may give rise to slow or noisy reconstructions, when a single λ value is considered for the entire iterative process. The aim of this work is to present a new implementation for the ART that takes into account a dynamic mode to calculate λ in DBT image reconstruction. A set of initial reconstructions of real phantom data was done using constant λ values. The results were used to choose, for each iteration, the suitable λ value, taking into account the image noise level and the convergence speed. A methodology to optimize λ automatically during the image reconstruction was proposed. Results showed we can dynamically choose λ values in such a way that the time needed to reconstruct the images can be significantly reduced (up to 70%) while achieving similar image quality. These results were confirmed with one clinical dataset. With simple methodology we were able to dynamically choose λ in DBT image reconstruction with ART, allowing a shorter image reconstruction time without increasing image noise. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
Gizatullin, Bulat; Neudert, Oliver; Stapf, Siegfried; Mattea, Carlos
2017-09-06
Dynamic nuclear polarization (DNP) is one of the most useful methods to increase sensitivity in NMR spectroscopy. It is based on the transfer of magnetization from an electron to the nuclear spin system. Based on previous work that demonstrated the feasibility of integrating DNP with fast field cycling (FFC) relaxometry and the possibility to distinguish between different mechanisms, such as the Overhauser effect (OE) and the solid effect (SE), the first FFC study of the differential relaxation properties of a copolymer is presented. For this purpose, concentrated solutions of the polystyrene-block-polybutadiene-block-polystyrene (SBS) triblock copolymer and the corresponding homopolymers were investigated. T1 -T2 relaxation data are discussed in terms of molecular mobility and the presence of radicals. The DNP selective data indicate a dominant SE contribution to the enhancement of the NMR signal for both blocks of the triblock copolymer and for the homopolymer solutions. The enhancement factors are different for both polymer types and in the copolymer, which is explained by the individual (1) H T1 relaxation times and different electron-nucleus coupling strength. The T1 relaxation dispersion measurements of the SE enhanced signal were performed, which led to improved signal-to-noise ratios that allowed the site-specific separation of relaxation times and their dependence on the Larmor frequency with a higher accuracy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A
2012-12-11
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.
The classical and quantum dynamics of molecular spins on graphene
Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo
2015-01-01
Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic1 and quantum computing2 devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics3,4, and electrical spin-manipulation4-11. However, the influence of the graphene environment on the spin systems has yet to be unraveled12. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets13 on graphene. While the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly-developed model. Coupling to Dirac electrons introduces a dominant quantum-relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully-coherent, resonant spin tunneling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin-manipulation in graphene nanodevices. PMID:26641019
Dynamic assembly of molecularly imprinted polymer nanoparticles.
Gong, Haiyue; Hajizadeh, Solmaz; Jiang, Lingdong; Ma, Huiting; Ye, Lei
2017-09-11
Manipulation of specific binding and recycling of materials are two important aspects for practical applications of molecularly imprinted polymers. In this work, we developed a new approach to control the dynamic assembly of molecularly imprinted nanoparticles by surface functionalization. Molecularly imprinted polymer nanoparticles with a well-controlled core-shell structure were synthesized using precipitation polymerization. The specific binding sites were created in the core during the first step imprinting reaction. In the second polymerization step, epoxide groups were introduced into the particle shell to act asan intermediate linker to immobilize phenylboronic acids, as well as to introduce cis-diol structures on surface. The imprinted polymer nanoparticles modified with boronic acid and cis-diol structures maintained high molecular binding specificity, and the nanoparticles could be induced to form dynamic particle aggregation that responded to pH variation and chemical stimuli. The possibility of modulating molecular binding and nanoparticle assembly in a mutually independent fashion can be exploited in a number of applications where repeated use of precious nanoparticles is needed. Copyright © 2017 Elsevier Inc. All rights reserved.
Sorokin, S. V.; Klimko, G. V.; Sedova, I. V.; Sitnikova, A. A.; Kirilenko, D. A.; Baidakova, M. V.; Yagovkina, M. A.; Komissarova, T. A.; Belyaev, K. G.; Ivanov, S. V.
2016-12-01
This paper presents a comprehensive study of structural, optical and electrical properties of heterostructures with linearly graded InxGa1-xAs metamorphic buffer layers (MBLs) grown by molecular beam epitaxy on GaAs (001) substrates. The low density of threading dislocations (well below 106 cm-2) in 1-μm-thick In0.3Ga0.7As layers grown atop of the linearly graded InxGa1-xAs/GaAs MBLs has been confirmed by using transmission electron microscopy (TEM). X-ray diffraction (XRD) data demonstrate good agreement between the experimentally measured In step-back and its calculations in the frames of existing models. Combining the XRD reciprocal space maps (RSM) of the structures and the spatially-resolved selective area electron diffraction measurements by cross-sectional TEM in depth-profiled RSM diagrams allowed direct visualization of the strain relaxation dynamics during the MBL growth. Strong effect of the azimuth angle and the value of an unintentional initial miscut of nominally (001) oriented GaAs substrate on the strain relaxation dynamics was observed.
Bazioti, C.; Papadomanolaki, E.; Kehagias, Th.; Walther, T.; Smalc-Koziorowska, J.; Pavlidou, E.; Komninou, Ph.; Karakostas, Th.; Iliopoulos, E.; Dimitrakopulos, G. P.
2015-10-01
We investigate the structural properties of a series of high alloy content InGaN epilayers grown by plasma-assisted molecular beam epitaxy, employing the deposition temperature as variable under invariant element fluxes. Using transmission electron microscopy methods, distinct strain relaxation modes were observed, depending on the indium content attained through temperature adjustment. At lower indium contents, strain relaxation by V-pit formation dominated, with concurrent formation of an indium-rich interfacial zone. With increasing indium content, this mechanism was gradually substituted by the introduction of a self-formed strained interfacial InGaN layer of lower indium content, as well as multiple intrinsic basal stacking faults and threading dislocations in the rest of the film. We show that this interfacial layer is not chemically abrupt and that major plastic strain relaxation through defect introduction commences upon reaching a critical indium concentration as a result of compositional pulling. Upon further increase of the indium content, this relaxation mode was again gradually succeeded by the increase in the density of misfit dislocations at the InGaN/GaN interface, leading eventually to the suppression of the strained InGaN layer and basal stacking faults.
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.
Yoo, Jejoong; Aksimentiev, Aleksei
2013-12-10
The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.
Atomic dynamics of alumina melt: A molecular dynamics simulation study
S.Jahn
2008-03-01
Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.
Molecular dynamics simulations of classical stopping power.
Grabowski, Paul E; Surh, Michael P; Richards, David F; Graziani, Frank R; Murillo, Michael S
2013-11-22
Molecular dynamics can provide very accurate tests of classical kinetic theory; for example, unambiguous comparisons can be made for classical particles interacting via a repulsive 1/r potential. The plasma stopping power problem, of great interest in its own right, provides an especially stringent test of a velocity-dependent transport property. We have performed large-scale (~10(4)-10(6) particles) molecular dynamics simulations of charged-particle stopping in a classical electron gas that span the weak to moderately strong intratarget coupling regimes. Projectile-target coupling is varied with projectile charge and velocity. Comparisons are made with disparate kinetic theories (both Boltzmann and Lenard-Balescu classes) and fully convergent theories to establish regimes of validity. We extend these various stopping models to improve agreement with the MD data and provide a useful fit to our results.
Characterization of Rare Events in Molecular Dynamics
Carsten Hartmann
2013-12-01
Full Text Available A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.
Study of Nanowires Using Molecular Dynamics Simulations
Monk, Joshua D
2007-01-01
In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...
Molecular dynamics modelling of solidification in metals
Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)
1997-12-31
Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.
Ottou Abe, M. T.; Correia, N. T.; Ndjaka, J. M. B.; Affouard, F.
2015-10-01
In this paper, structural and dynamical properties of ibuprofen and ketoprofen glass-forming liquids have been investigated by means of molecular dynamics simulations. Molecular mobility of both materials is analyzed with respect to the different inter-molecular linear/cyclic hydrogen bonding associations. For ibuprofen, the dominant organization is found to be composed of small hydrogen bonding aggregates corresponding to cyclic dimers through the carboxyl group. For ketoprofen, the propensity of cyclic dimers is significantly reduced by the formation of hydrogen bonds with the ketone oxygen of the molecule altering the hydrogen bond (HB) associating structures that can be formed and thus molecular dynamics. The issue of the presence/absence of the peculiar low frequency Debye-type process in dielectric relaxation spectroscopy (DRS) data in these materials is addressed. Results obtained from simulations confirm that the Debye process originates from the internal cis-trans conversion of the —COOH carboxyl group. It is shown that the specific intermolecular HB structures associated to a given profen control the main dynamical features of this conversion, in particular its separation from the α-process, which make it detectable or not from DRS. For ibuprofen, the possible role of the —CCCO torsion motion, more "local" than the —COOH motion since it is less influenced by the intermolecular HBs, is suggested in the microscopic origin of the quite intense secondary γ-relaxation process detected from DRS.
Magnetohydrodynamics dynamical relaxation of coronal magnetic fields. III. 3D spiral nulls
Fuentes-Fernández, J.; Parnell, C. E.
2012-08-01
Context. The majority of studies on stressed 3D magnetic null points consider magnetic reconnection driven by an external perturbation, but the formation of a genuine current sheet equilibrium remains poorly understood. This problem has been considered more extensively in two dimensions, but lacks a generalization into 3D fields. Aims: 3D magnetic nulls are more complex than 2D nulls and the field can take a greater range of magnetic geometries local to the null. Here, we focus on one type and consider the dynamical non-resistive relaxation of 3D spiral nulls with initial spine-aligned current. We aim to provide a valid magnetohydrostatic equilibrium, and describe the electric current accumulations in various cases, involving a finite plasma pressure. Methods: A full MHD code was used, with the resistivity set to zero so that reconnection is not allowed, to run a series of experiments in which a perturbed spiral 3D null point was allowed to relax towards an equilibrium via real, viscous damping forces. Changes to the initial plasma pressure and other magnetic parameters were systematically investigated. Results: For the axisymmetric case, the evolution of the field and the plasma is such that it concentrates the current density into two cone-shaped regions along the spine, thus concentrating the twist of the magnetic field around the spine, leaving a radial configuration in the fan plane. The plasma pressure redistributes to maintain the current density accumulations. However, it is found that changes in the initial plasma pressure do not significantly modify the final state. In the cases where the initial magnetic field is not axisymmetric, an infinite-time singularity of current perpendicular to the fan is found at the location of the null.
Greene, Patrick T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Schofield, Samuel P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Nourgaliev, Robert [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2016-06-21
A new mesh smoothing method designed to cluster mesh cells near a dynamically evolving interface is presented. The method is based on weighted condition number mesh relaxation with the weight function being computed from a level set representation of the interface. The weight function is expressed as a Taylor series based discontinuous Galerkin projection, which makes the computation of the derivatives of the weight function needed during the condition number optimization process a trivial matter. For cases when a level set is not available, a fast method for generating a low-order level set from discrete cell-centered elds, such as a volume fraction or index function, is provided. Results show that the low-order level set works equally well for the weight function as the actual level set. Meshes generated for a number of interface geometries are presented, including cases with multiple level sets. Dynamic cases for moving interfaces are presented to demonstrate the method's potential usefulness to arbitrary Lagrangian Eulerian (ALE) methods.
Superfluidity and relaxation dynamics of a laser-stirred two-dimensional Bose gas
Singh, Vijay Pal; Weitenberg, Christof; Dalibard, Jean; Mathey, Ludwig
2017-04-01
We investigate the superfluid behavior of a two-dimensional (2D) Bose gas of 87Rb atoms using classical field dynamics. In the experiment by R. Desbuquois et al. [Nat. Phys. 8, 645 (2012), 10.1038/nphys2378], a 2D quasicondensate in a trap is stirred with a blue-detuned laser beam along a circular path around the trap center. Here, we study this experiment from a theoretical perspective. The heating induced by stirring increases rapidly above a velocity vc, which we define as the critical velocity. We identify the superfluid, the crossover, and the thermal regime by a finite, a sharply decreasing, and a vanishing critical velocity, respectively. We demonstrate that the onset of heating occurs due to the creation of vortex-antivortex pairs. A direct comparison of our numerical results to the experimental ones shows a good agreement, if a systematic shift of the critical phase-space density is included. We relate this shift to the absence of thermal equilibrium between the condensate and the thermal wings, which were used in the experiment to extract the temperature. We expand on this observation by studying the full relaxation dynamics between the condensate and the thermal cloud.
T. Stensitzki
2016-07-01
Full Text Available We combined femtosecond (fs VIS pump–IR probe spectroscopy with fs VIS pump–supercontinuum probe spectroscopy to characterize the photoreaction of the hexacoordinated Al(tpfc-Br8(py2 in a comprehensive way. Upon fs excitation at ∼400 nm in the Soret band, the excitation energy relaxes with a time constant of (250 ± 80 fs to the S2 and S1 electronic excited states. This is evident from the rise time of the stimulated emission signal in the visible spectral range. On the same time scale, narrowing of broad infrared signals in the C=C stretching region around 1500 cm−1 is observed. Energy redistribution processes are visible in the vibrational and electronic dynamics with time constants between ∼2 ps and ∼20 ps. Triplet formation is detected with a time constant of (95 ± 3 ps. This is tracked by the complete loss of stimulated emission. Electronic transition of the emerging triplet absorption band overlaps considerably with the singlet excited state absorption. In contrast, two well separated vibrational marker bands for triplet formation were identified at 1477 cm−1 and at 1508 cm−1. These marker bands allow a precise identification of triplet dynamics in corrole systems.
Kozlowska, M; Kozlowska, Marzena; Kutner, Ryszard
2006-01-01
We analyse the dynamics of the Warsaw Stock Exchange index WIG at a daily time horizon before and after its well defined local maxima of the cusp-like shape decorated with oscillations. The rising and falling paths of the index peaks can be described by the Mittag-Leffler function superposed with various types of oscillations. The latter is a solution of our model of index dynamics defined by the nonhomogeneous fractional relaxation equation. This solution is a generalised analog of an exactly solvable model of viscoelastic materials. We found that the Warsaw Stock Exchange can be considered as an intermediate system lying between two complex ones, defined by short and long-time limits of the Mittag-Leffler function; these limits are given by the Kohlraush-Williams-Watts law for the initial times, and the power-law or the Nutting law for asymptotic time. Hence follows the corresponding short- and long-time power-law behaviour (different universality classes) of the time-derivative of the logarithm of WIG whic...
Sappey, R; Ocio, M; Hammann, J
2000-01-01
We discuss here the nature of the low-temperature magnetic relaxation in samples of magnetic nanoparticles. In addition to usual magnetic viscosity measurement, we have used the residual memory ratio (RMR) method. This procedure enables us to overcome the uncertainties usually associated with the energy barrier distribution, thus giving a more detailed insight on the nature of the observed dynamics. A custom-made apparatus coupling dilution refrigeration and SQUID magnetometry allowed measurements of very diluted samples at temperatures ranging between 60 mK and 7 K. Two types of particles have been studied: gamma-Fe sub 2 O sub 3 of moderate anisotropy, and CoFe sub 2 O sub 4 of higher anisotropy where quantum effects are more likely to occur. In both cases, the data cannot simply be interpreted in terms of mere thermally activated dynamics of independent particles. The deviation from thermal activation seems to go opposite of what is expected from the possible effect of particle interactions. We therefore b...
Schwartz, Benjamin Joel [Univ. of California, Berkeley, CA (United States)
1992-11-01
The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured and effects of external hydrogen-bonding interactions on the proton transfer are studied. The proton transfer takes place in ~240 fsec in nonpolar environments, but becomes faster than instrumental resolution of 110 fsec in methanol solution. The dynamics following photodissociation of CH_{2}I_{2} and other small molecules provide the first direct observations of geminate recombination. The recombination of many different photodissociating species occurs on a ~350 fsec time scale. Results show that recombination yields but not rates depend on the solvent environment and suggest that recombination kinetics are dominated by a single collision with surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. Data show no simple correlation between hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes, implying that the isomerization does not provide a suitable for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial steps of the photochromic reaction process occur extremely rapidly. Laser system and computer codes for data analysis are discussed.
Little evidence for dynamic divergences in ultraviscous molecular liquids
Hecksher, Tina; Nielsen, Albena; Olsen, Niels Boye
2008-01-01
The physics of the ultraviscous liquid phase preceding glass formation continues to pose major problems that remain unsolved. It is actively debated, for instance, whether the marked increase of the relaxation time reflects an underlying phase transition to a state of infinite relaxation time. To...... shows that there is no compelling evidence for the Vogel-Fulcher-Tammann (VFT) prediction that the relaxation time diverges at a finite temperature.We conclude that theories with a dynamic divergence of the VFT formlack a direct experimental basis....
Monoamine transporters: Insights from molecular dynamics simulations
Julie eGrouleff
2015-10-01
Full Text Available The human monoamine transporters facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia and Parkinson’s disease. Inhibition of the monoamine transporters is thus an important strategy for treatment of such diseases. The monoamine transporters are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the monoamine transporters, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.
Bead-Fourier path integral molecular dynamics
Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto
2003-06-01
Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.
Monoamine transporters: insights from molecular dynamics simulations
Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit
2015-01-01
The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185
Nonequilibrium molecular dynamics theory, algorithms and applications
Todd, Billy D
2017-01-01
Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...
Molecular dynamics study of the mechanical loss in amorphous pure and doped silica
Hamdan, Rashid; Trinastic, Jonathan P.; Cheng, H. P., E-mail: cheng@qtp.ufl.edu [Department of Physics and Quantum Theory Project, University of Florida, Gainesville, Florida 32611 (United States)
2014-08-07
Gravitational wave detectors and other precision measurement devices are limited by the thermal noise in the oxide coatings on the mirrors of such devices. We have investigated the mechanical loss in amorphous oxides by calculating the internal friction using classical, atomistic molecular dynamics simulations. We have implemented the trajectory bisection method and the non-local ridge method in the DL-POLY molecular dynamics simulation software to carry out those calculations. These methods have been used to locate the local potential energy minima that a system visits during a molecular dynamics trajectory and the transition state between any two consecutive minima. Using the numerically calculated barrier height distributions, barrier asymmetry distributions, relaxation times, and deformation potentials, we have calculated the internal friction of pure amorphous silica and silica mixed with other oxides. The results for silica compare well with experiment. Finally, we use the numerical calculations to comment on the validity of previously used theoretical assumptions.
Peterseim, Tobias; Dressel, Martin
2017-01-01
The time-dependent optical properties of molecular systems are investigated by step-scan Fourier-transform spectroscopy in order to explore the dynamics at phase transitions and molecular orientation in the milli- and microsecond range. The electrical switching of liquid crystals traced by vibrational spectroscopy reveals a rotation of the molecules with a relaxation time of 2 ms. The photo-induced neutral-ionic transition in TTF-CA takes place by a suppression of the dimerization in the ionic phase and creation of neutral domains. The time-dependent infrared spectra, employed to investigate the domain-wall dynamics, depend on temperature and laser pulse intensity; the relaxation of the spectra follows a stretched-exponential decay with relaxation times in the microsecond range strongly dependent on temperature and laser intensity. We present all details of the experimental setups and thoroughly discuss the technical challenges.
Peterseim, Tobias; Dressel, Martin
2016-06-01
The time-dependent optical properties of molecular systems are investigated by step-scan Fourier-transform spectroscopy in order to explore the dynamics at phase transitions and molecular orientation in the milli- and microsecond range. The electrical switching of liquid crystals traced by vibrational spectroscopy reveals a rotation of the molecules with a relaxation time of 2 ms. The photo-induced neutral-ionic transition in TTF-CA takes place by a suppression of the dimerization in the ionic phase and creation of neutral domains. The time-dependent infrared spectra, employed to investigate the domain-wall dynamics, depend on temperature and laser pulse intensity; the relaxation of the spectra follows a stretched-exponential decay with relaxation times in the microsecond range strongly dependent on temperature and laser intensity. We present all details of the experimental setups and thoroughly discuss the technical challenges.
Control-volume representation of molecular dynamics.
Smith, E R; Heyes, D M; Dini, D; Zaki, T A
2012-05-01
A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ϑ(i) for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [Todd et al., Phys. Rev. E 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.
Learning generative models of molecular dynamics.
Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J
2012-01-01
We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 regularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories.
Dynamic Maintenance and Visualization of Molecular Surfaces
Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N
2004-12-16
Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.
Molecular dynamics simulations of magnetized dusty plasmas
Piel, Alexander; Reichstein, Torben; Wilms, Jochen
2012-10-01
The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)
Application of optimal prediction to molecular dynamics
Barber, IV, John Letherman [Univ. of California, Berkeley, CA (United States)
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is δ-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
Three-stage classical molecular dynamics model for simulation of heavy-ion fusion
Godre Subodh S.
2015-01-01
Full Text Available A three-stage Classical Molecular Dynamics (3S-CMD approach for heavy-ion fusion is developed. In this approach the Classical Rigid-Body Dynamics simulation for heavy-ion collision involving light deformed nucleus is initiated on their Rutherford trajectories at very large initial separation. Collision simulation is then followed by relaxation of the rigid-body constrains for one or both the colliding nuclei at distances close to the barrier when the trajectories of all the nucleons are obtained in a Classical Molecular Dynamics approach. This 3S-CMD approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but also the internal vibrational excitations of one or both the nuclei at distances close to the barrier. The results of the dynamical simulation for 24Mg+208Pb collision show significant modification of the fusion barrier and calculated fusion cross sections due to internal excitations.
Effect of solvent model when probing protein dynamics with molecular dynamics.
Genheden, Samuel
2017-01-01
We probe the dynamics of the Bpti and Galectin-3 proteins using molecular dynamics simulations employing three water models at different levels of resolution, viz. the atomistic TIP4P-Ewald, the coarse-grained Elba and an implicit generalised Born model. The dynamics are quantified indirectly by model-free order parameters, S(2) of the backbone NH and selected side-chain bond vectors, which also have been determined experimentally through NMR relaxation measurements. For the backbone, the order parameters produced with the three solvent models agree to a large extent with experiments, giving average unsigned deviations between 0.03 and 0.06. For the side-chains, for which the experimental data is incomplete, the deviations are considerably larger with mean deviations between 0.13 and 0.17. However, for both backbone and side-chains, it is difficult to pick a winner, as all models perform equally well overall. For a more complete set of side-chain vectors, we resort to analysing the variation among the estimates from different solvent models. Unfortunately, the variations are found to be sizeable with mean deviations between 0.11 and 0.15. Implications for computational assessment of protein dynamics are discussed.
Molecular motions and phase transitions. NMR relaxation times studies of several lecithins.
Bar-Adon, R; Gilboa, H
1981-01-01
The spin-lattice relaxation time, T1, and the dipolar energy relaxation time, TD, were measured as a function of temperature. The materials studied were samples of anhydrous L-dipalmitoyl lecithin, DL-dipalmitoyl lecithin, L-dimyristoyl lecithin, DL-dimyristoyl lecithin and their monohydrates, and of anhydrous egg yolk lecithin. It is shown that TD is a much more sensitive parameter than T1 for the determination of the Chapman phase transition. Comparison between T1 and TD provides informatio...
Luchinat, Claudio; Parigi, Giacomo
2007-02-07
Since the recent availability of high sensitivity field-cycling relaxometers, it has become possible to measure the protein proton relaxation in millimolar protein solutions as a function of magnetic field. In principle, this provides direct access to the so-called spectral density function of protein protons and, hence, to a full set of dynamic parameters. Understanding the dynamic behavior of biological molecules is increasingly appreciated as crucial to understanding their function. However, theoretical tools to analyze the collective relaxation behavior of protons in solute macromolecules over a wide range of magnetic fields are lacking. A complete relaxation matrix analysis of such behavior is described here. This analysis provides excellent predictions of the experimental proton magnetization decays/recoveries-measured to an unprecedented level of accuracy by a last-generation fast field-cycling relaxometer-of two different globular proteins, hen egg white lysozyme and human serum albumin. The new experimentally validated theoretical model is then used to extract dynamic information on these systems. A "collective" order parameter SC2, different from, but complementary to, that commonly extracted from heteronuclear relaxation measurements at high field, is defined and measured. An accurate estimate of the rotational correlation time is obtained: in the case of lysozyme it agrees very well with theoretical predictions; in the case of serum albumin it provides evidence for aggregation at millimolar concentration.
Nerkararyan, Khachatur V; Bozhevolnyi, Sergey I
2015-01-01
We investigate the relaxation dynamics of a quantum dipole emitter (QDE), e.g., a molecule or quantum dot, located near a metal nanoparticle (MNP) exhibiting a dipolar localized surface plasmon (LSP) resonance at the frequency of the QDE radiative transition. A generic three-level QDE, which is pumped with an external laser pulse and thereby brought into an optically active excited state, is considered to be weakly coupled to the resonant LSP described by a coherent state. It is shown that, under the condition of the QDE-MNP characteristic relaxation time being much shorter than that of the QDE in free space but much longer than the LSP lifetime, the QDE relaxation dynamics can be described analytically and feature, in general, non-exponential decay with complicated transient behaviour. The main physical consequence of this relaxation process is that the emission, being largely determined by the MNP, comes out with a substantial delay. It is also shown that energy dissipation in the QDE-MNP system is relatively weak with the probability of the photon emission being ∼0.75, a number which, rather surprisingly, does not explicitly depend on the metal absorption characteristics. A large number of QDE-MNP system parameters in our analytical description open new possibilities for controlling quantum emitter dynamics.
Molecular dynamics simulation of irradiation damage in tungsten
Park, Na-Young [School of Advanced Materials Engineering, Kookmin University, Seoul 136-702 (Korea, Republic of); Kim, Yu-Chan; Seok, Hyun-Kwang; Han, Seung-Hee [Advanced Metals Research Center, Korea Institute of Science and Technology (KIST), Seoul 136-791 (Korea, Republic of); Cho, Seungyon [Reactor Engineering Team, Division of Research and Development, National Fusion Research Center, Daejeon 305-333 (Korea, Republic of); Cha, Pil-Ryung [School of Advanced Materials Engineering, Kookmin University, Seoul 136-702 (Korea, Republic of)], E-mail: cprdream@kookmin.ac.kr
2007-12-15
Molecular dynamics (MD) simulations have been performed for the radiation damage of tungsten using a modified Finnis-Sinclair type many-body interatomic potential. The interstitial defects and vacancies are distinguished by the Wigner-Seitz cell method and the types of the interstitial dumbbells are also identified by the azimuth and polar angles of dumbbell line vectors. It is observed that the number of interstitial defects and vacancies initially sharply increases and passing through the peak position, relaxes to the steady state for all PKA energies and that all residual interstitial dumbbells at the steady state are the <1 1 1>-oriented. Based on the variation of the orientation angles of dumbbells during the radiation damage simulation, it is found that the recombination of the <1 1 1>-oriented dumbbells with the vacancies is much faster than that of two other types of dumbbells and that the population of the <1 0 0> dumbbells is much larger than that of the <1 1 0> ones in spite of its higher formation energy, the reason of which is explained with the dynamics of the individual dumbbell.
Horke, Daniel A; Roberts, Gareth M; Verlet, Jan R R
2011-08-04
The spectroscopy and ultrafast relaxation dynamics of excited states of the radical anion of a representative charge-transfer acceptor molecule, 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, have been studied in the gas phase using time-resolved photoelectron spectroscopy. The photoelectron spectra reveal that at least two anion excited states are bound. Time-resolved studies show that both excited states are very short-lived and internally convert to the anion ground state, with the lower energy state relaxing within 200 fs and a near-threshold valence-excited state relaxing on a 60 fs time scale. These excited states, and in particular the valence-excited state, present efficient pathways for electron-transfer reactions in the highly exergonic inverted region which commonly displays rates exceeding predictions from electron-transfer theory.
Saha, Leton C.; Mian, Shabeer A.; Kim, Hyo Jeong; Saha, Joyanta K.; Matin, Mohammad A.; Jang, Joon Kyung [Pusan National University, Miryang (Korea, Republic of)
2011-02-15
We investigated how temperature influences the structural and energetic dynamics of carbon nanotubes (CNTs) undergoing a high-speed impact with a Si (110) surface. By performing molecular dynamics simulations in the temperature range of 100 - 300 K, we found that a low temperature CNT ends up with a higher vibrational energy after collision than a high temperature CNT. The vibrational temperature of CNT increases by increasing the surface temperature. Overall, the structural and energy relaxation of low temperature CNTs are faster than those of high temperature CNTs.
Langevin equation with colored noise for constant-temperature molecular dynamics simulations.
Ceriotti, Michele; Bussi, Giovanni; Parrinello, Michele
2009-01-16
We discuss the use of a Langevin equation with a colored (correlated) noise to perform constant-temperature molecular dynamics. Since the equations of motion are linear in nature, it is easy to predict the response of a Hamiltonian system to such a thermostat and to tune at will the relaxation time of modes of different frequency. This allows one to optimize the time needed for equilibration and to generate independent configurations. We show how this frequency-dependent response can be exploited to control the temperature of Car-Parrinello-like dynamics without affecting the adiabatic separation of the electronic degrees of freedom from the vibrations of the ions.
Govind, Chinju; Karunakaran, Venugopal
2017-04-13
Hemin is a unique model compound of heme proteins carrying out variable biological functions. Here, the excited state relaxation dynamics of heme model compounds in the ferric form are systematically investigated by changing the axial ligand (Cl/Br), the peripheral substituent (vinyl/ethyl-meso), and the solvent (methanol/DMSO) using femtosecond pump-probe spectroscopy upon excitation at 380 nm. The relaxation time constants of these model compounds are obtained by global analysis. Excited state deactivation pathway of the model compounds comprising the decay of the porphyrin excited state (S*) to ligand to metal charge transfer state (LMCT, τ1), back electron transfer from metal to ligand (MLCT, τ2), and relaxation to the ground state through different electronic spin states of iron (τ3 and τ4) are proposed along with the vibrational cooling processes. This is based on the excited state absorption spectral evolution, similarities between the transient absorption spectra of the ferric form and steady state absorption spectra of the low-spin ferrous form, and the data analysis. The observation of an increase of all the relaxation time constants in DMSO compared to the methanol reflects the stabilization of intermediate states involved in the electronic relaxation. The transient absorption spectra of met-myoglobin are also measured for comparison. Thus, the transient absorption spectra of these model compounds reveal the involvement of multiple iron spin states in the electronic relaxation dynamics, which could be an alternative pathway to the ground state beside the vibrational cooling processes and associated with the inherent features of the heme b type.
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Relaxation dynamics of the conductive processes in BaTiO{sub 3} ceramics at high temperature
Leyet, Y., E-mail: yuri@cnt.uo.edu.cu [Departamento de Fisica, Facultad de Ciencias Naturales. Universidad de Oriente, Santiago de Cuba, C.P. 90500 (Cuba); Guerrero, F. [Departamento de Fisica, Facultad de Ciencias Naturales. Universidad de Oriente, Santiago de Cuba, C.P. 90500 (Cuba); Perez de la Cruz, J. [INESCPorto, Rua do Campo Alegre, 687, 4169-007, Porto (Portugal)
2010-07-25
The temperature and frequency dependences of the undoped BaTiO{sub 3} ceramics dielectric properties were measured between 25 deg. C and 700 deg. C and 100 Hz to 10 MHz, respectively. A dielectric anomaly was observed at low frequencies in the temperature range of 400-700 deg. C. This anomaly was associated to a low frequency dispersion process taking place at high temperature. The relaxation dynamics of the conductive process in BaTiO{sub 3} ceramics was investigated. A relaxation function in the time domain ({Phi}(t)) was determined from the frequency dependence of the dielectric modulus, using a relaxation function in the frequency domain (F*({omega})). In BaTiO{sub 3} ceramics context, the best relaxation functions (F*({omega})), in the temperature ranges of 220-400 deg. C and 425 deg. C and 630 deg. C, were found to be a Cole-Cole and Davidson-Cole distribution functions, respectively. The relaxation function (f(t)) obtained by the time domain method was found to be a Kohlrausch-Williams-Watts (KWW) function type. The activation energy values (0.72 eV and 0.8 eV) reveal a mechanism correlated with the movement of single ionized oxygen vacancies and electrons of the second level of ionization, probably due to the formation of a titanium liquid phase during the sintering process.
McCune, Matthew; Kosztin, Ioan
2013-03-01
Cellular Particle Dynamics (CPD) is a theoretical-computational-experimental framework for describing and predicting the time evolution of biomechanical relaxation processes of multi-cellular systems, such as fusion, sorting and compression. In CPD, cells are modeled as an ensemble of cellular particles (CPs) that interact via short range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through numerical integration of their equations of motion. Here we present CPD simulation results for the fusion of both spherical and cylindrical multi-cellular aggregates. First, we calibrate the relevant CPD model parameters for a given cell type by comparing the CPD simulation results for the fusion of two spherical aggregates to the corresponding experimental results. Next, CPD simulations are used to predict the time evolution of the fusion of cylindrical aggregates. The latter is relevant for the formation of tubular multi-cellular structures (i.e., primitive blood vessels) created by the novel bioprinting technology. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.
Molecular dynamics studies of aromatic hydrocarbon liquids
McLaughlin, E.; Gupta, S.
1990-01-01
This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules.
Molecular dynamics in high electric fields
Apostol, M.; Cune, L. C.
2016-06-01
Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called "dipolons"); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.
Attosecond VUV Coherent Control of Molecular Dynamics
Ranitovic, P; Riviere, P; Palacios, A; Tong, X M; Toshima, N; Gonzalez-Castrillo, A; Martin, L; Martin, F; Murnane, M M; Kapteyn, H C
2014-01-01
High harmonic light sources make it possible to access attosecond time-scales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized. This is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep ultraviolet, which have not yet been synthesized. Here, we present a novel approach using attosecond vacuum ultraviolet pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly-ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipula...
Molecular Dynamics Studies of Nanofluidic Devices
Zambrano Rodriguez, Harvey Alexander
in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...... in transport caused by the walls become more dominant and the fluid consists of fewer molecules. Carbon nanotubes are tubular graphite molecules which can be imagined to function as nanoscale pipes or conduits. Another important material for nanofluidics applications is silica. Nowadays, silica nanochannels...... of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...
Arntsen, Christopher; Chen, Chen; Voth, Gregory A.
2017-09-01
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.
Molecular Dynamics: New Frontier in Personalized Medicine.
Sneha, P; Doss, C George Priya
2016-01-01
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.
[Oligoglycine surface structures: molecular dynamics simulation].
Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V
2010-01-01
The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.
Implementing peridynamics within a molecular dynamics code.
Lehoucq, Richard B.; Silling, Stewart Andrew; Plimpton, Steven James; Parks, Michael L.
2007-12-01
Peridynamics (PD) is a continuum theory that employs a nonlocal model to describe material properties. In this context, nonlocal means that continuum points separated by a finite distance may exert force upon each other. A meshless method results when PD is discretized with material behavior approximated as a collection of interacting particles. This paper describes how PD can be implemented within a molecular dynamics (MD) framework, and provides details of an efficient implementation. This adds a computational mechanics capability to an MD code, enabling simulations at mesoscopic or even macroscopic length and time scales.
Exchange frequency in replica exchange molecular dynamics
Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.
2008-01-01
The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.
Extension of Isospin Dependent Quantum Molecular Dynamics
FengZhaoqing; ZhangFengshou; LiWenfei; JinGenming
2003-01-01
Isospin dependent molecular dynamics (IQMD) has been used with success for studying isospin effects in heavy ion collisions at intermediate energies[1,2]. However, this model meets difficulty to study heavy ion collisions at low energies near Coulomb barrier since unsuitable dealing with the deformation, such as surface term induced by deformation during approaching projectile and target, which is not important at high energies, and it results in the calculated cross sections with IQMD which are much smaller than the experimental data at low energies. In this report, we propose a new method in which the surface term in the mean field is included in a proper way, the switch function method.
Molecular Dynamics Simulations of Interface Failure
Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.
2007-03-01
The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
Charge transport network dynamics in molecular aggregates
Jackson, Nicholas E. [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry; Chen, Lin X. [Argonne National Lab. (ANL), Argonne, IL (United States). Chemical Science and Engineering Division; Ratner, Mark A. [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry
2016-07-20
Due to the nonperiodic nature of charge transport in disordered systems, generating insight into static charge transport networks, as well as analyzing the network dynamics, can be challenging. Here, we apply time-dependent network analysis to scrutinize the charge transport networks of two representative molecular semiconductors: a rigid n-type molecule, perylenediimide, and a flexible p-type molecule, bBDT(TDPP)2. Simulations reveal the relevant timescale for local transfer integral decorrelation to be ~100 fs, which is shown to be faster than that of a crystalline morphology of the same molecule. Using a simple graph metric, global network changes are observed over timescales competitive with charge carrier lifetimes. These insights demonstrate that static charge transport networks are qualitatively inadequate, whereas average networks often overestimate network connectivity. Finally, a simple methodology for tracking dynamic charge transport properties is proposed.
Bauer, Florian, E-mail: fbauer@ecm.ub.e [HEP Group, Dept. ECM and Institut de Ciencies del Cosmos, Univ. de Barcelona, Av. Diagonal 647, E-08028 Barcelona, Catalonia (Spain); Sola, Joan, E-mail: sola@ecm.ub.e [HEP Group, Dept. ECM and Institut de Ciencies del Cosmos, Univ. de Barcelona, Av. Diagonal 647, E-08028 Barcelona, Catalonia (Spain); Stefancic, Hrvoje, E-mail: shrvoje@thphys.irb.h [Theoretical Physics Division, Rudjer Boskovic Institute, PO Box 180, HR-10002 Zagreb (Croatia)
2010-05-10
We present an unconventional approach for addressing the old cosmological constant (CC) problem in a class of F(R,G) models of modified gravity. For a CC of arbitrary size and sign the corresponding cosmological evolution follows an expansion history which strikingly resembles that of our real universe. The effects of the large CC are relaxed dynamically and there is no fine-tuning at any stage. In addition, the relaxation mechanism alleviates the coincidence problem. The upshot is that a large cosmological constant and the observed cosmic expansion history coexist peacefully in the Relaxed Universe. This model universe can be thought of as an interesting preliminary solution of the cosmological constant problem, in the sense that it provides a successful dynamical mechanism able to completely avoid the fine-tuning problem (the toughest aspect of the CC problem). However, since the Relaxed Universe is formulated within the context of modified gravity, it may still suffer of some of the known issues associated with these theories, and therefore it can be viewed only as a toy-model proposal towards a final solution of the CC problem.
Klameth, F; Henritzi, P; Vogel, M
2014-04-14
We perform molecular dynamics simulations to study static and dynamic length scales in molecular supercooled liquids, in particular, water. For a determination of these scales, we use equilibrium configurations and pin appropriate subsets of molecules so as to obtain random matrices, cylindrical pores, and slit confinements. Static length scales ξ(s) are determined by analyzing overlap correlation functions for various fractions of pinned molecules or distances to the confining walls. For water in all confinements and for propylene oxide trimers in random geometry, a linear increase of ξ(s) with inverse temperature is found. Dynamic length scales ξ(d) are determined by analogous analysis of fraction-dependent or position-resolved correlation times of structural relaxation. While ξ(d) continuously grows upon cooling in the cylindrical and slit confinements, we find no evidence for a temperature dependence in random matrices, implying that molecular dynamics in parsed volumes is qualitatively different from that in bulk liquids. Finally, we study possible connections between the growth of the static and dynamic length scales and the slowdown of the structural relaxation of the supercooled bulk liquids. For water, we observe a linear relation between ln τ(α) and ξ(s)²/T in the whole accessible range down to the critical temperature of mode-coupling theory, T(c). In the weakly supercooled regime, the same relation holds also for ξ(d), as obtained from cylindrical and slit confinements, but deviations from this behavior are observed near T(c). The results are discussed in connection with random first-order theory and experimental studies of liquid dynamics in nanoscopic confinements and binary mixtures.
Adrjanowicz, K; Kaminski, K; Wlodarczyk, P; Grzybowska, K; Tarnacka, M; Zakowiecki, D; Garbacz, G; Paluch, M; Jurga, S
2013-10-07
This paper presents comprehensive studies on the molecular dynamics of a pharmaceutically important substance, posaconazole. In order to characterize relaxation dynamics in the supercooled liquid and glassy states, dielectric and mechanical spectroscopies were applied. Dielectric data have indicated multiple relaxation processes that appear above and below the glass transition temperature Tg (τα=100 s) of posaconazole. From the curvature of the dielectric log10(τα) versus inverse of temperature dependence, we determine so-called "fragility", being a very popular parameter for classifying the structural dynamics of supercooled liquids and polymers. From the calculations, we get m=150, which means that is one of the most fragile glass-forming liquids. In this paper, the relaxation dynamics of supercooled posaconazole extracted from the dielectric response function was also confronted with shear-mechanical relaxation. Finally, we have also presented a direct comparison of the fragility and the number of dynamically correlated molecules Nc determined from dynamic calorimetry curves and dielectric and mechanical spectroscopies, showing a clear deviation in the picture of glass-transition dynamics generated by calorimetric and spectroscopic techniques.
1H relaxation dispersion in solutions of nitroxide radicals: Influence of electron spin relaxation
Kruk, D.; Korpała, A.; Kubica, A.; Kowalewski, J.; Rössler, E. A.; Moscicki, J.
2013-03-01
The work presents a theory of nuclear (1H) spin-lattice relaxation dispersion for solutions of 15N and 14N radicals, including electron spin relaxation effects. The theory is a generalization of the approach presented by Kruk et al. [J. Chem. Phys. 137, 044512 (2012)], 10.1063/1.4736854. The electron spin relaxation is attributed to the anisotropic part of the electron spin-nitrogen spin hyperfine interaction modulated by rotational dynamics of the paramagnetic molecule, and described by means of Redfield relaxation theory. The 1H relaxation is caused by electron spin-proton spin dipole-dipole interactions which are modulated by relative translational motion of the solvent and solute molecules. The spectral density characterizing the translational dynamics is described by the force-free-hard-sphere model. The electronic relaxation influences the 1H relaxation by contributing to the fluctuations of the inter-molecular dipolar interactions. The developed theory is tested against 1H spin-lattice relaxation dispersion data for glycerol solutions of 4-oxo-TEMPO-d16-15N and 4-oxo-TEMPO-d16-14N covering the frequency range of 10 kHz-20 MHz. The studies are carried out as a function of temperature starting at 328 K and going down to 290 K. The theory gives a consistent overall interpretation of the experimental data for both 14N and 15N systems and explains the features of 1H relaxation dispersion resulting from the electron spin relaxation.
SPILADY: A parallel CPU and GPU code for spin-lattice magnetic molecular dynamics simulations
Ma, Pui-Wai; Dudarev, S. L.; Woo, C. H.
2016-10-01
Spin-lattice dynamics generalizes molecular dynamics to magnetic materials, where dynamic variables describing an evolving atomic system include not only coordinates and velocities of atoms but also directions and magnitudes of atomic magnetic moments (spins). Spin-lattice dynamics simulates the collective time evolution of spins and atoms, taking into account the effect of non-collinear magnetism on interatomic forces. Applications of the method include atomistic models for defects, dislocations and surfaces in magnetic materials, thermally activated diffusion of defects, magnetic phase transitions, and various magnetic and lattice relaxation phenomena. Spin-lattice dynamics retains all the capabilities of molecular dynamics, adding to them the treatment of non-collinear magnetic degrees of freedom. The spin-lattice dynamics time integration algorithm uses symplectic Suzuki-Trotter decomposition of atomic coordinate, velocity and spin evolution operators, and delivers highly accurate numerical solutions of dynamic evolution equations over extended intervals of time. The code is parallelized in coordinate and spin spaces, and is written in OpenMP C/C++ for CPU and in CUDA C/C++ for Nvidia GPU implementations. Temperatures of atoms and spins are controlled by Langevin thermostats. Conduction electrons are treated by coupling the discrete spin-lattice dynamics equations for atoms and spins to the heat transfer equation for the electrons. Worked examples include simulations of thermalization of ferromagnetic bcc iron, the dynamics of laser pulse demagnetization, and collision cascades.
Lasoroski, Aurélie; Vuilleumier, Rodolphe; Pollet, Rodolphe
2014-07-07
The electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zero-field-splitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zero-field-splitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zero-field-splitting was significantly influenced by this substitution.
Dynamic relaxation processes in compressible multiphase flows. Application to evaporation phenomena
Le Métayer O.
2013-07-01
Full Text Available Phase changes and heat exchanges are examples of physical processes appearing in many industrial applications involving multiphase compressible flows. Their knowledge is of fundamental importance to reproduce correctly the resulting effects in simulation tools. A fine description of the flow topology is thus required to obtain the interfacial area between phases. This one is responsible for the dynamics and the kinetics of heat and mass transfer when evaporation or condensation occurs. Unfortunately this exchange area cannot be obtained easily and accurately especially when complex mixtures (drops, bubbles, pockets of very different sizes appear inside the transient medium. The natural way to solve this specific trouble consists in using a thin grid to capture interfaces at all spatial scales. But this possibility needs huge computing resources and can be hardly used when considering physical systems of large dimensions. A realistic method is to consider instantaneous exchanges between phases by the way of additional source terms in a full non-equilibrium multiphase flow model [2,15,17]. In this one each phase obeys its own equation of state and has its own set of equations and variables (pressure, temperature, velocity, energy, entropy,.... When enabling the relaxation source terms the multiphase mixture instantaneously tends towards a mechanical or thermodynamic equilibrium state at each point of the flow. This strategy allows to mark the boundaries of the real flow behavior and to magnify the dominant physical effects (heat exchanges, evaporation, drag,... inside the medium. A description of the various relaxation processes is given in the paper. Les changements de phase et les transferts de chaleur sont des exemples de phénomènes physiques présents dans de nombreuses applications industrielles faisant intervenir des écoulements compressibles multiphasiques. La connaissance des mécanismes associés est primordiale afin de reproduire
Molecular Dynamics Simulations of Janus Particle Dynamics in Uniform Flow
Archereau, Aurelien Y M; Willmott, Geoff R
2016-01-01
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the solid-liquid interaction over their surfaces and calculate the forces and torques experienced by the particles as a function of their orientation with respect to the flow. We also examine particles that are deformed slightly from a spherical shape. We compare the simulation results to the predictions of a previously introduced theoretical approach, which computes the forces and torques on particles with variable slip lengths or aspherical deformations that are much smaller than the particle radius. We find that there is good agreement between the forces and torques computed from our simulations and the theoretical predictions, when the slip condition is applied to the first layer of liquid molecules adjacent to the surface.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations
Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.
2016-10-01
SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
Understanding mechanical properties of polymer nanocomposites with molecular dynamics simulations
Sen, Suchira
Equilibrium Molecular Dynamics (MD) simulations are used extensively to study various aspects of polymer nanocomposite (PNC) behavior in the melt state---the key focus is on understanding mechanisms of mechanical reinforcement. Mechanical reinforcement of the nanocomposite is believed to be caused by the formation of a network-like structure---a result of polymer chains bridging particles to introduce network elasticity. In contrast, in traditional composites, where the particle size range is hundreds of microns and high loadings of particle are used, the dominant mechanism is the formation of a percolated filler structure. The difference in mechanism with varying particle sizes, at similar particle loading, arises from the polymer-particle interfacial area available, which increases dramatically as the particle size decreases. Our interest in this work is to find (a) the kind of polymer-particle interactions necessary to facilitate the formation of a polymer network in a nanocomposite, and (b) the reinforcing characteristics of such a polymer network. We find that very strong polymer-particle binding is necessary to create a reinforcing network. The strength of the binding has to be enough to immobilize polymer on the particle surface for timescales comparable and larger than the terminal relaxation time of the stress of the neat melt. The second finding, which is a direct outcome of very strong binding, is that the method of preparation plays a critical role in determining the reinforcement of the final product. The starting conformations of the polymer chains determine the quality of the network. The strong binding traps the polymer on the particle surface which gets rearranged to a limited extent, within stress relaxation times. Significant aging effects are seen in system relaxation; the inherent non-equilibrium consequences of such strong binding. The effect of the polymer immobilization slows down other relaxation processes. The diffusivity of all chains is
Accelerated molecular dynamics simulations of protein folding.
Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew
2015-07-30
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.
Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation
Singh, Raghvendra Pratap; Cleri, Fabrizio
2013-01-01
We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to...
Dynamic Wetting on Graphene-Coated Surface: Molecular Dynamics Investigation
Hung, Shih-Wei; Shiomi, Junichiro
2015-11-01
Wettability of graphene-coated surface gained significant attention recently due to discussion on the ``transparency'' (whether the wetting characteristics follow that of graphene or the underlying surface) and practical applications of graphene. In terms of static contact angle, the wettability of graphene-coated surfaces have been widely studied by experiments, simulations, and theory in recent years. However, the studies of dynamic wetting on graphene-coated surfaces are limited. In the present study, molecular dynamics simulation was performed to study the dynamic wetting of water droplet on graphene-coated surfaces from a microscopic point of view. The results show that the degree of similarity between the spreading behavior on graphene-coated surface and that on pure graphene (or that on the underlying surface) depends on time, i.e. how nonequilibrium the interface dynamics is. We also found that this feature can be altered by introducing defects into graphene. The work is partially supported by Grant-in-Aid for JSPS Fellows 26-04364 and JST CREST.
Glowacki, David R., E-mail: drglowacki@gmail.com [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Department of Computer Science, University of Bristol, Bristol BS8 1UB (United Kingdom); PULSE Institute and Department of Chemistry, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Orr-Ewing, Andrew J. [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Harvey, Jeremy N. [Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Belgium)
2015-07-28
We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD{sub 3}CN → DF + CD{sub 2}CN reaction in CD{sub 3}CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD{sub 3}CN solvent, equilibrium power spectra of DF in CD{sub 3}CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol{sup −1} localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD{sub 3}CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational
Nonomura, Yoshihiko
2014-11-01
Nonequilibrium relaxation behaviors in the Ising model on a square lattice based on the Wolff algorithm are totally different from those based on local-update algorithms. In particular, the critical relaxation is described by the stretched-exponential decay. We propose a novel scaling procedure to connect nonequilibrium and equilibrium behaviors continuously, and find that the stretched-exponential scaling region in the Wolff algorithm is as wide as the power-law scaling region in local-update algorithms. We also find that relaxation to the spontaneous magnetization in the ordered phase is characterized by the exponential decay, not the stretched-exponential decay based on local-update algorithms.
Dynamics of Star Polymers in Fast Extensional Flow and Stress Relaxation
Huang, Qian; Agostini, Serena; Hengeller, Ludovica
2016-01-01
We confirm the observation from Ianniruberto and Marrucci [ Macromolecules 2013, 46, 267-275 ] that entangled melts of branched polystyrenes behave like linear polystyrenes in the steady state of fast extensional flow, by measuring a linear, an asymmetric star, and a symmetric star polystyrene wi...... they relax in a similar way, most likely via arm retraction, at short time, but behave differently at long time due to both the length of the arm and the branch point. The terminal relaxation is described by a Doi and Edwards based model, i.e., considering pure orientational relaxation....
Webber, J Beau W; Anderson, Ross; Strange, John H; Tohidi, Bahman
2007-05-01
The Gibbs-Thomson effect modifies the pressure and temperature at which clathrates occur, hence altering the depth at which they occur in the seabed. Nuclear magnetic resonance (NMR) measurements as a function of temperature are being conducted for water/ice/hydrate systems in a range of pore geometries, including templated SBA-15 silicas, controlled pore glasses and sol-gel silicas. Rotator-phase plastic ice is shown to be present in confined geometry, and bulk tetrahydrofuran hydrate is also shown to probably have a rotator phase. A novel NMR cryoporometry protocol, which probes both melting and freezing events while avoiding the usual problem of supercooling for the freezing event, has been developed. This enables a detailed probing of the system for a given pore size and geometry and the exploration of differences between hydrate formation and dissociation processes inside pores. These process differences have an important effect on the environment, as they impact on the ability of a marine hydrate system to re-form once warmed above a critical temperature. Ab initio quantum-mechanical molecular dynamics calculations are also being employed to probe the dynamics of liquids in pores at nanometric dimensions.
D. A. Horke; Roberts, G.M.; Verlet, J. R. R.
2011-01-01
The spectroscopy and ultrafast relaxation dynamics of excited states of the radical anion of a representative charge-transfer acceptor molecule, 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, have been studied in the gas phase using time-resolved photoelectron spectroscopy. The photoelectron spectra reveal that at least two anion excited states are bound. Time-resolved studies show that both excited states are very short-lived and internally convert to the anion ground state, with the ...
Jurjiu, Aurel; Galiceanu, Mircea; Farcasanu, Alexandru; Chiriac, Liviu; Turcu, Flaviu
2016-12-01
In this paper, we focus on the relaxation dynamics of Sierpinski hexagon fractal polymer. The relaxation dynamics of this fractal polymer is investigated in the framework of the generalized Gaussian structure model using both Rouse and Zimm approaches. In the Rouse-type approach, by performing real-space renormalization transformations, we determine analytically the complete eigenvalue spectrum of the connectivity matrix. Based on the eigenvalues obtained through iterative algebraic relations we calculate the averaged monomer displacement and the mechanical relaxation moduli (storage modulus and loss modulus). The evaluation of the dynamical properties in the Rouse-type approach reveals that they obey scaling in the intermediate time/frequency domain. In the Zimm-type approach, which includes the hydrodynamic interactions, the relaxation quantities do not show scaling. The theoretical findings with respect to scaling in the intermediate domain of the relaxation quantities are well supported by experimental results.
The 2011 Dynamics of Molecular Collisions Conference
Nesbitt, David J. [JILA, NIST
2011-07-11
The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor
Kumar, P Padma; Kalinichev, Andrey G; Kirkpatrick, R James
2009-01-22
A comprehensive Car-Parrinello molecular dynamics (CP-MD) study of aqueous solutions of carbonic acid (H(2)CO(3)), bicarbonate (HCO(3)(-)), carbonate (CO(3)(2-)), and carbon dioxide (CO(2)) provides new quantitative insight into the structural and dynamic aspects of the hydrogen-bonding environments for these important aqueous species and their effects on the structure, H-bonding, and dynamical behavior of the surrounding water molecules. The hydration structures of the different carbonate species depend on their ability to accept and donate H-bonds with H(2)O. The H-bonds donated by the C-O-H sites of the carbonate species to water molecules are generally stronger and longer-lived than those accepted by these sites from water molecules. The structural relaxation among the water molecules is dominated by diffusional (translational) motion of H(2)O, whereas the H-bond reorganization is dominated by the librational motion of the water molecules and the carbonate species. The rates of structural relaxation of the H(2)O molecules and the rates of H-bond reorganization among them are slower in systems containing carbonate species, consistent with previous studies of simple salt solutions. The strengths and lifetimes of H-bonds involving the carbonate species positively correlate with the total negative charge on the species. H-bond donation from H(2)O to CO(2) is weak, but the presence of CO(2) noticeably affects the structure and structural relaxation of the surrounding H-bonding network leading to generally stronger H-bonds and slower relaxation rates, the behavior typical of a hydrophobic solute.
Zerbetto, Mirco; Buck, Matthias; Meirovitch, Eva; Polimeno, Antonino
2011-01-20
An integrated computational methodology for interpreting NMR spin relaxation in proteins has been developed. It combines a two-body coupled-rotator stochastic model with a hydrodynamics-based approach for protein diffusion, together with molecular dynamics based calculations for the evaluation of the coupling potential of mean force. The method is applied to ¹⁵N relaxation of N-H bonds in the Rho GTPase binding (RBD) domain of plexin-B1, which exhibits intricate internal mobility. Bond vector dynamics are characterized by a rhombic local ordering tensor, S, with principal values S₀² and S₂², and an axial local diffusion tensor, D₂, with principal values D(2,||) and D(2,⊥). For α-helices and β-sheets we find that S₀² ~ -0.5 (strong local ordering), -1.2 computational approach for treating NMR relaxation in proteins by combining stochastic modeling and molecular dynamics. The approach developed provides new insights by its application to a protein that experiences complex dynamics.
Molecular structures and intramolecular dynamics of pentahalides
Ischenko, A. A.
2017-03-01
This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.
Can molecular dynamics help in understanding dielectric phenomena?
Olmi, Roberto; Bittelli, Marco
2017-01-01
Molecular dynamics (MD) is a modeling technique widely used in material science as well as in chemical physics, biochemistry and biophysics. MD is based on ‘first principles’, allowing one to compute the physical characteristics of a material, such as density, heat capacity, isothermal compressibility and also the dielectric constant and relaxation, mixing a classical physics approach and statistical mechanics. Although a number of papers exist in the literature concerning the study of the dielectric properties of liquid and solid materials, the MD approach appears to be almost ignored in the electromagnetic aquametry community. We use a rather simple example, a mixture of ethanol and water at various concentrations, to introduce MD as a theoretical tool for investigating the dielectric behavior of more complex moist substances. We show that MD simulations suggest a time-domain model for alcohol-water solutions, consisting in a mixture of a KWW stretched-exponential and a simple exponential, whose validity could be subjected to an experimental verification.
Stresses and elastic constants of crystalline sodium, from molecular dynamics
Schiferl, S.K.
1985-02-01
The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the results to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs.
Atomistic Molecular Dynamics Simulations of Shock Compressed Quartz
Farrow, Matthew R
2011-01-01
Atomistic non-equilibrium molecular dynamics (NEMD) simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer and van Santen to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geom- etry optimised system of a polar slab in a 3-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under repres...
B. K Bihari
2014-03-01
Full Text Available The shelf life of a composite solid propellant is one of the critical aspects for the usage of solid propellants. To assess the ageing behavior of the composite solid propellant, the activation energy is a key parameter. The activation energy is determined by analysis of visco-elastic response of the composite solid propellant when subjected to sinusoidal excitation. In the present study, dynamic mechanical analyzer was used to characterize six different types of propellants based on hydroxyl terminated polybutadiene, aluminium, ammonium perchlorate cured with toluene diisocyanate having burning rates varying from 5 mm/s to 25 mm/s at 7000 kPa. Each propellant sample was given a multi-frequency strain of 0.01 percent at three discrete frequencies (3.5 Hz, 11 Hz, 35 Hz in the temperature range -80 °C to + 80 °C. It was observed that all the propellants have shown two relaxation events (α- and β- transition in the temperature range -80 °C to +80 °C. The α-transition was observed between -66 °C and -51 °C and β-transition between 7 °C and 44 °C for the propellants studied. The activation energy for both transitions was determined by Arrhenius plot from dynamic properties measured at different frequencies and also by time temperature superposition principle using Williams-Landel-Ferry and Arrhenius temperature dependence equations. The data reveal that the activation energy corresponding to α-transition varies from 90 kJ/mol to 125 kJ/mol for R-value between 0.7 to 0.9 while for β-transition the values are from 75 kJ/mol to 92 kJ/mol. The activation energy corresponding to β-transition may be used to predict the useful life of solid propellant.Defence Science Journal, 2014, 64(2, pp. 173-178. DOI: http://dx.doi.org/10.14429/dsj.64.3818
Molecular Dynamics Simulations and XAFS (MD-XAFS)
Schenter, Gregory K.; Fulton, John L.
2017-01-20
MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.
Dielectric Properties of Poly(ethylene oxide) from Molecular Dynamics Simulations
Smith, Grant D.
1994-01-01
The order, conformations and dynamics of poly(oxyethylene) (POE) melts have been investigated through molecular dynamics simulations. The potential energy functions were determined from detailed ab initio electronic structure calculations of the conformational energies of the model molecules 1,2-dimethoxyethane (DME) and diethylether. The x-ray structure factor for POE from simulation will be compared to experiment. In terms of conformation, simulations reveal that chains are extended in the melt relative to isolated chains due to the presence of strong intermolecular O...H interactions, which occur at the expense of intramolecular O...H interactions. Conformational dynamics about the C-C bond were found to be significantly faster than in polymethylene, while conformational dynamics about the C-O bond even faster than the C-C dynamics. The faster local dynamics in POE relative to polymethylene is consistent with C-13 NMR spin-lattice relaxation experiments. Conformational transitions showed significant second-neighbor correlation, as was found for polymethylene. This correlation of transitions with C-C neighbors was found to be reduced relative to C-O neighbors. Dielectric relaxation from simulation will also be compared with experiment.
DMS: A Package for Multiscale Molecular Dynamics
Somogyi, Endre; Ortoleva, Peter J
2013-01-01
Advances in multiscale theory and computation provide a novel paradigm for simulating many-classical particle systems. The Deductive Multiscale Simulator (DMS) is a multiscale molecular dynamics (MD) program built on two of these advances, i.e., multiscale Langevin (ML) and multiscale factorization (MF). Both capture the coevolution of the the coarse-grained (CG) state and the microstate. This provides these methods with great efficiency over conventional MD. Neither involve the introduction of phenomenological governing equations for the CG state with attendant uncertainty in both their form of the governing equations and the data needed to calibrate them. The design and implementation of DMS as an open source computational platform is presented here. DMS is written in Python, uses Gromacs to achieve the microphase, and then advances the microstate via a CG-guided evolution. DMS uses MDAnalysis, a Python library for analyzing MD trajectories, to perform computations required to construct CG-related variables...
Molecular Dynamics Simulations for Predicting Surface Wetting
Jing Chen
2014-06-01
Full Text Available The investigation of wetting of a solid surface by a liquid provides important insights; the contact angle of a liquid droplet on a surface provides a quantitative measurement of this interaction and the degree of attraction or repulsion of that liquid type by the solid surface. Molecular dynamics (MD simulations are a useful way to examine the behavior of liquids on solid surfaces on a nanometer scale. Thus, we surveyed the state of this field, beginning with the fundamentals of wetting calculations to an examination of the different MD methodologies used. We highlighted some of the advantages and disadvantages of the simulations, and look to the future of computer modeling to understand wetting and other liquid-solid interaction phenomena.
Molecular Dynamics Simulations of Hypervelocity Impacts
Owens, Eli T.; Bachlechner, Martina E.
2007-03-01
Outer space silicon solar cells are exposed to impacts with micro meteors that can destroy the surface leading to device failure. A protective coating of silicon nitride will protect against such failure. Large-scale molecular dynamics simulations are used to study how silicon/silicon nitride fails due to hypervelocity impacts. Three impactors made of silicon nitride are studied. Their cross-sectional areas, relative to the target, are as follows: the same as the target, half of the target, and a quarter of the target. Impactor speeds from 5 to 11 km/second yield several modes of failure, such as deformation of the target by the impactor and delimitation of the silicon nitride from the silicon at the interface. These simulations will give a much clearer picture of how solar cells composed of a silicon/silicon nitride interface will respond to impacts in outer space. This will ultimately lead to improved devices with longer life spans.
Molecular dynamics simulation of laser shock phenomena
Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).
2001-10-01
Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)
Nanodrop contact angles from molecular dynamics simulations
Ravipati, Srikanth; Aymard, Benjamin; Yatsyshin, Petr; Galindo, Amparo; Kalliadasis, Serafim
2016-11-01
The contact angle between three phases being in thermodynamic equilibrium is highly sensitive to the nature of the intermolecular forces as well as to various fluctuation effects. Determining the Young contact angle of a sessile drop sitting on a substrate from molecular dynamics (MD) simulations is a highly non-trivial task. Most commonly employed methods for finding droplet contact angles from MD simulation data either require large numbers of particles or are system-dependent. We propose a systematic geometry based methodology for extracting the contact angle from simulated sessile droplets by analysing an appropriately coarse-grained density field. To demonstrate the method, we consider Lennard-Jones (LJ) and SPC/E water nanodroplets of different sizes sitting on planar LJ walls. Our results are in good agreement with Young contact angle values computed employing test-area perturbation method.
Molecular dynamics study of ice structural evolution
Wang Yan; Dong Shun-Le
2008-01-01
Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of～1.0GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H...O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.
Nano-tribology through molecular dynamics simulations
王慧; 胡元中; 邹鲲; 冷永胜
2001-01-01
The solidification and interfacial slip in nanometer-scale lubricating films as well as the contact and adhesion of metal crystals have been studied via molecular dynamics simulations. Results show that the critical pressure for the solid-liquid transition declines as the film thickness decreases, in-dicating that the lubricant in the thin films may exist in a solid-like state. It is also found that the interfa-cial slip may occur in thin films at relatively low shear rate, and there is a good correlation between the slip phenomenon and the lubricant solidification. The simulations reveal that a micro-scale adhesion may take place due to the atomic jump during the process of approaching or separating of two smooth crystal surfaces, which provides important information for understanding the origin of interfacial friction.
Oesterling, Sven; Schalk, Oliver; Geng, Ting; Thomas, Richard D; Hansson, Tony; de Vivie-Riedle, Regina
2017-01-18
For the series furan, furfural and β-furfural we investigated the effect of substituents and their positioning on the photoinduced relaxation dynamics in a combined theoretical and experimental approach. Using time resolved photoelectron spectroscopy with a high intensity probe pulse, we can, for the first time, follow the whole deactivation process of furan through a two photon probe signal. Using the extended 2-electron 2-orbital model [Nenov et al., J. Chem. Phys., 2011, 135, 034304] we explain the formation of one central conical intersection and predict the influence of the aldehyde group of the derivatives on its geometry. This, as well as the relaxation mechanisms from photoexcitation to the final outcome was investigated using a variety of theoretical methods. Complete active space self consistent field was used for on-the-fly calculations while complete active space perturbation theory and coupled cluster theory were used to accurately describe critical configurations. Experiment and theory show the relaxation dynamics of furfural and β-furfural to be slowed down, and together they disclose an additional deactivation pathway, which is attributed to the nO lonepair state introduced with the aldehyde group.
Molecular beam studies of reaction dynamics
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Molecular-dynamic study of liquid ethylenediamine
Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.
2016-10-01
Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.
A molecular dynamics approach to barrodiffusion
Cooley, James; Marciante, Mathieu; Murillo, Michael
2016-10-01
Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin
Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.
Ogata, S.
1998-01-27
Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.
Magnetic relaxation dynamics driven by the first-order character of magnetocaloric La(Fe,Mn,Si)13.
Lovell, Edmund; Bratko, Milan; Caplin, A David; Barcza, Alexander; Katter, Matthias; Ghivelder, Luis; Cohen, Lesley F
2016-08-13
Here, we study the temporal evolution of the magnetic field-driven paramagnetic to ferromagnetic transition in the La(Fe,Mn,Si)13 material family. Three compositions are chosen that show varying strengths of the first-order character of the transition, as determined by the relative magnitude of their magnetic hysteresis and temperature separation between the zero-field transition temperature Tc and the temperature Tcrit, where the transition becomes continuous. Systematic variations in the fixed field, isothermal rate of relaxation are observed as a function of temperature and as a function of the degree of first-order character. The relaxation rate is reduced in more weakly first-order compositions and is also reduced as the temperature is increased towards Tcrit At temperatures above Tcrit, the metastability of the transition vanishes along with its associated temporal dynamics.This article is part of the themed issue 'Taking the temperature of phase transitions in cool materials'.
Turton, David A; Hunger, Johannes; Stoppa, Alexander; Hefter, Glenn; Thoman, Andreas; Walther, Markus; Buchner, Richard; Wynne, Klaas
2009-08-12
We have measured the intermolecular dynamics of the 1,3-dialkylimidazolium-based room-temperature ionic liquids (RTILs) [emim][BF(4)], [emim][DCA], and [bmim][DCA] at 25 degrees C from below 1 GHz to 10 THz by ultrafast optical Kerr effect (OKE) spectroscopy and dielectric relaxation spectroscopy (DRS) augmented by time-domain terahertz and far-infrared FTIR spectroscopy. This concerted approach allows a more detailed analysis to be made of the relatively featureless terahertz region, where the higher frequency diffusional modes are strongly overlapped with librations and intermolecular vibrations. Of greatest interest though, is an intense low frequency (sub-alpha) relaxation that we show is in accordance with recent simulations that have reported mesoscopic structure arising from aggregates or clusters--structure that explains the anomalous and inconveniently high viscosities of these liquids.
Chen, Y. [Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Zhuang, G.; Ross, P.N. [Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Van Hove, M.A.; Fadley, C.S. [Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)]|[Department of Physics, University of California at Davis, Davis, California 95616 (United States)
1998-10-01
The equivalent-core approximation is implemented in a novel way so as to calculate core-level relaxation energies in photoelectron spectroscopy. The method is based on self-consistent field (SCF) Hartree{endash}Fock molecular-orbital calculations via linear combinations of atomic orbitals, and involves evaluating the difference of sums of two-electron Coulomb and exchange integrals, for all electrons in an atom and in its equivalent-core ion. By thus avoiding SCF calculations with a core hole present (the true final state of photoemission), this procedure is shown to significantly save computing time in comparison with an exact SCF direct-hole calculation. Application of the method in single atoms and selected molecules shows about a 10{percent} difference with respect to direct-hole calculation results. The approximation introduces about 1{endash}6 eV errors compared to the experimental results of gas phase molecules. This method thus should be a generally useful procedure for estimating relaxation energies in core spectra. {copyright} {ital 1998 American Institute of Physics.}
Approximation of quantum observables by molecular dynamics simulations
Sandberg, Mattias
2016-01-06
In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.
Cruzeiro, E. Zambrini; Tiranov, A.; Usmani, I.; Laplane, C.; Lavoie, J.; Ferrier, A.; Goldner, P.; Gisin, N.; Afzelius, M.
2017-05-01
We present a detailed study of the lifetime of optical spectral holes due to population storage in Zeeman sublevels of Nd3 +:Y2SiO5 . The lifetime is measured as a function of magnetic field strength and orientation, temperature, and Nd3 + doping concentration. At the lowest temperature of 3 K we find a general trend where the lifetime is short at low field strengths, then increases to a maximum lifetime at a few hundred mT, and then finally decays rapidly for high field strengths. This behavior can be modeled with a relaxation rate dominated by Nd3 +-Nd3 + cross relaxation at low fields and spin lattice relaxation at high magnetic fields. The maximum lifetime depends strongly on both the field strength and orientation, due to the competition between these processes and their different angular dependencies. The cross relaxation limits the maximum lifetime for concentrations as low as 30 ppm of Nd3 + ions. By decreasing the concentration to less than 1 ppm we could completely eliminate the cross relaxation, reaching a lifetime of 3.8 s at 3 K. At higher temperatures the spectral hole lifetime is limited by the magnetic-field-independent Raman and Orbach processes. In addition we show that the cross relaxation rate can be strongly reduced by creating spectrally large holes of the order of the optical inhomogeneous broadening. Our results are important for the development and design of new rare-earth-ion doped crystals for quantum information processing and narrow-band spectral filtering for biological tissue imaging.
Dynamic Behaviour of Vortex Matter, Memory Effect and Mittag－Leffier Relaxation
LIU Gang; HAN Ru-Shan
2001-01-01
Using fractional Fokker-Planck equation and Langevin equation's Monte Carlo simulation, we find that when current density is less than critical current density, at the very beginning the motion for vortices is mainly within the pinning well with the typical relaxation time Tr. When time t is longer than Tr, the vortex glass will distort between two adjacent pining wells and will lead to memory effect which is lacking in the Mott insulator and pancake vortices. The inertial effect is not dominating as compared with the formation and growth of easy-flow channels. The random quenched disorder will lead to Mittag-Leffler relaxation.
Busselez, Rémi; Cerclier, Carole V; Ndao, Makha; Ghoufi, Aziz; Lefort, Ronan; Morineau, Denis
2014-10-07
A prototypical Gay Berne discotic liquid crystal was studied by means of molecular dynamics simulations both in the bulk state and under confinement in a nanoporous channel. The phase behavior of the confined system strongly differs from its bulk counterpart: the bulk isotropic-to-columnar transition is replaced by a continuous ordering from a paranematic to a columnar phase. Moreover, a new transition is observed at a lower temperature in the confined state, which corresponds to a reorganization of the intercolumnar order. It reflects the competing effects of pore surface interaction and genuine hexagonal packing of the columns. The translational molecular dynamics in the different phases has been thoroughly studied and discussed in terms of collective relaxation modes, non-Gaussian behavior, and hopping processes.
LDA and molecular dynamics determination of Ag deposition onto (1 0 0) surfaces in silicon
Mazzone, A.M
2003-03-20
This study analyzes the effects of the surface morphology on the deposition of Ag onto Si using LDA and isothermal molecular dynamics. The (1 0 0) silicon surface has either a bulk termination or the dimerization pattern experimentally observed. Small clusters representing a section of these surfaces have been used in LDA calculations to find preferred adsorption sites. Isothermal molecular dynamics describe the motions of the diffusing adatoms in a temperature range from T=10 to 1000 K. Both calculations indicate that Ag and Si do not mix and the deposited structure is formed by linear chains located in the trench between surface atoms. However, MD calculations show that, due to the relaxation of the surface and to thermal lattice vibrations, the stable state of the deposited atoms may considerably differ from the one calculated from LDA. This result has both a practical and a methodological significance.
Nonadiabatic excited-state molecular dynamics: On-the-fly limiting of essential excited states
Nelson, Tammie; Naumov, Artem; Fernandez-Alberti, Sebastian; Tretiak, Sergei
2016-12-01
The simulation of nonadiabatic dynamics in extended molecular systems involving hundreds of atoms and large densities of states is particularly challenging. Nonadiabatic coupling terms (NACTs) represent a significant numerical bottleneck in surface hopping approaches. Rather than using unreliable NACT cutting schemes, here we develop "on-the-fly" state limiting methods to eliminate states that are no longer essential for the non-radiative relaxation dynamics as a trajectory proceeds. We propose a state number criteria and an energy-based state limit. The latter is more physically relevant by requiring a user-imposed energy threshold. For this purpose, we introduce a local kinetic energy gauge by summing contributions from atoms within the spatial localization of the electronic wavefunction to define the energy available for upward hops. The proposed state limiting schemes are implemented within the nonadiabatic excited-state molecular dynamics framework to simulate photoinduced relaxation in poly-phenylene vinylene (PPV) and branched poly-phenylene ethynylene (PPE) oligomers for benchmark evaluation.
Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure
2014-08-30
properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to
Kaminski, K; Adrjanowicz, K; Wojnarowska, Z; Grzybowska, K; Hawelek, L; Paluch, M; Zakowiecki, D; Mazgalski, J
2011-07-01
Cryomilling was applied to obtain amorphous forms of the base ziprasidone and its hydrochloride salt. Complete amorphization of both samples was confirmed by differential scanning calorimetry and X-ray measurements. As it turned out, cryogrinding is very effective way to obtain these drugs in the amorphous state, especially because melting of both ziprazidones accompanies significant chemical decomposition as revealed by ultra performance liquid chromatography examination. Consequently, the glassy state cannot be reached in conventional way, that is, by supercooling of melt. Broadband dielectric relaxation measurements were performed on both drugs to describe their molecular dynamics above as well as below their glass transition temperatures (T(g)). We found out that ziprasidone base and its hydrochloride salt differ in T(g) in the same way as it was previously reported for tramadol monohydrate and its hydrochloride. Moreover, our dielectric studies revealed that molecular mobility is not the main factor controlling kinetics of crystallization of both ziprasidones above their T(g) . Below the T(g) relaxation related to water as well as secondary relaxation process originating from the intermolecular interaction (Johari-Goldstein) were identified in the loss spectra of both materials. We have demonstrated that except of local mobility, water is the dominant factor moving both ziprasidones toward recrystallization process. Finally, we have also carried out solubility measurements to show that dissolution rate of the amorphous ziprasidones is much higher with respect to the crystalline samples.
Backbone dynamics of the EIAV-Tat protein from {sup 15}N relaxation studies
Ejchart, A.; Herrmann, F.; Roesch, P.; Sticht, H.; Willbold, D. [Bayreuth Univ., Bayreuth (Germany)
1994-12-31
The work investigates the mobility of EIAV-Tat protein backbone by measuring the relaxation parameters of the {sup 15}N nitrogens. High degree of the flexibility, non-typical of rigid, well structured proteins was shown. 3 refs, 2 figs.
Alexandrov, N.A.; Marinova, K.G.; Gurkov, T.D.; Danov, K.D.; Kralchevsky, P.A.; Stoyanov, S.D.; Blijdenstein, T.B.J.; Arnaudov, L.N.; Pelan, E.G.; Lips, A.
2012-01-01
The pendant-drop method (with drop-shape analysis) and Langmuir trough are applied to investigate the characteristic relaxation times and elasticity of interfacial layers from the protein HFBII hydrophobin. Such layers undergo a transition from fluid to elastic solid films. The transition is
Nanoscale deicing by molecular dynamics simulation
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-07-01
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice
How Dynamic Visualization Technology Can Support Molecular Reasoning
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
Molecular Dynamics Studies of Energy Transfer Processes in Crystal Systems.
1984-11-30
Computer molecular dynamics studies have been carried out on the problem of attaining a fundamental understanding of shock-induced initiation of...intramolecular energy exchange in shock-loaded systems are presented. Originator-supplied keywords include: Molecular dynamics , Energy transfer, Shock front, Shock wave, Explosives, Shock structure.
How Dynamic Visualization Technology Can Support Molecular Reasoning
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
A Multiscalling Constant Lambda Molecular Dynamic Gromacs Implementation
Goga, Nicolae; Costache, Stefania; Marrink, Siewert
2009-01-01
Molecular dynamics is one of the methods used now-a-days by the scientific community to study the property of polymers. This paper presents a new method for multiscaling molecular dynamics that combines the advantages of fine-grained and coarse grained representations. The new methodology is
Interfacial effects revealed by ultrafast relaxation dynamics in BiFeO 3 / YBa 2 Cu 3 O 7 bilayers
Springer, D.
2016-02-12
The temperature dependence of the relaxation dynamics in the bilayer thin film heterostructure composed of multiferroic BiFeO3 (BFO) and superconducting YBa2Cu3O7 (YBCO) grown on a (001) SrTiO3 substrate is studied by a time-resolved pump-probe technique, and compared with that of pure YBCO thin film grown under the same growth conditions. The superconductivity of YBCO is found to be retained in the heterostructure. We observe a speeding up of the YBCO recombination dynamics in the superconducting state of the heterostructure, and attribute it to the presence of weak ferromagnetism at the BFO/YBCO interface as observed in magnetization data. An extension of the Rothwarf-Taylor model is used to fit the ultrafast dynamics of BFO/YBCO, that models an increased quasiparticle occupation of the ferromagnetic interfacial layer in the superconducting state of YBCO.
Non-radiative relaxation dynamics of pyrrole following excitation in the range 249.5-200 nm
Kirkby, Oliver M.; Parkes, Michael A.; Neville, Simon P.; Worth, Graham A.; Fielding, Helen H.
2017-09-01
The non-radiative relaxation dynamics of pyrrole have been investigated using time-resolved photoelectron spectroscopy and quantum dynamics simulations. Following excitation of the A2 (11 πσ∗) state, we observe population flow out of the Franck-Condon region on a ≲ 50 fs timescale. Following excitation of the B2 (21 ππ∗) state, we observe population being transferred to the A2 (11 πσ∗) state on a <50 fs timescale and subsequently out of the Franck-Condon region, also on a <50 fs timescale. Quantum dynamics calculations suggest that population is transferred from the B2 (21 ππ∗) state through the A2 (1 π 3pz) state to the B1 (21 πσ∗) state before being transferred to the A2 (11 πσ∗) state.
Roed, Lisa Anita; Niss, Kristine; Jakobsen, Bo
2015-01-01
The frequency dependent specific heat has been measured under pressure for the molecular glass forming liquid 5-polyphenyl-4-ether in the viscous regime close to the glass transition. The temperature and pressure dependences of the characteristic time scale associated with the specific heat...
Zhang, Rui; Schweizer, Kenneth S
2012-04-21
We generalize the microscopic naïve mode coupling and nonlinear Langevin equation theories of the coupled translation-rotation dynamics of dense suspensions of uniaxial colloids to treat the effect of applied stress on shear elasticity, cooperative cage escape, structural relaxation, and dynamic and static yielding. The key concept is a stress-dependent dynamic free energy surface that quantifies the center-of-mass force and torque on a moving colloid. The consequences of variable particle aspect ratio and volume fraction, and the role of plastic versus double glasses, are established in the context of dense, glass-forming suspensions of hard-core dicolloids. For low aspect ratios, the theory provides a microscopic basis for the recently observed phenomenon of double yielding as a consequence of stress-driven sequential unlocking of caging constraints via reduction of the distinct entropic barriers associated with the rotational and translational degrees of freedom. The existence, and breadth in volume fraction, of the double yielding phenomena is predicted to generally depend on both the degree of particle anisotropy and experimental probing frequency, and as a consequence typically occurs only over a window of (high) volume fractions where there is strong decoupling of rotational and translational activated relaxation. At high enough concentrations, a return to single yielding is predicted. For large aspect ratio dicolloids, rotation and translation are always strongly coupled in the activated barrier hopping event, and hence for all stresses only a single yielding process is predicted.
Kumar, Manindra; Tiwari, Tuhina; Chauhan, Jagdish Kumar; Srivastava, Neelam
2014-12-01
The ion dynamics and relaxation behavior of a novel polymer electrolyte system is studied by presenting impedance spectroscopy data in a different formalism. The prepared system has conductivity of the order of 10-3 Scm-1 at 303 K, and the RH % = 55. Depressed Nyquist plots and broadened M˝ curves (as a function of ω) indicated the distribution of the relaxation time, which is further confirmed by the fractional value of the Kohlrausch-William-Watts (KWW) function (β ˜ 0.75). The hopping and caged movement of the ions are observed in the experimental frequency range (˜MHz), which is confirmed by the conductivity and dielectric representations. The scaling of the conductivity data, with reference to salt concentration and temperature, are successfully observed by fitting the conductivity data exclusively in the Jonscher Power Law (JPL) region. An inverse relation between τcon and σ indicated a strong correlation between the ion and polymer segment motion. An additional high frequency relaxation phenomenon is observed at 50% of the salt concentration, which is correlated with the self-diffusion of the ion and proposed that such phenomenon is observed when ions have multiplet forming tendency.
Nanoscale deicing by molecular dynamics simulation.
Xiao, Senbo; He, Jianying; Zhang, Zhiliang
2016-08-14
Deicing is important to human activities in low-temperature circumstances, and is critical for combating the damage caused by excessive accumulation of ice. The aim of creating anti-icing materials, surfaces and applications relies on the understanding of fundamental nanoscale ice adhesion mechanics. Here in this study, we employ all-atom modeling and molecular dynamics simulation to investigate ice adhesion. We apply force to detach and shear nano-sized ice cubes for probing the determinants of atomistic adhesion mechanics, and at the same time investigate the mechanical effect of a sandwiched aqueous water layer between ice and substrates. We observe that high interfacial energy restricts ice mobility and increases both ice detaching and shearing stresses. We quantify up to a 60% decrease in ice adhesion strength by an aqueous water layer, and provide atomistic details that support previous experimental studies. Our results contribute quantitative comparison of nanoscale adhesion strength of ice on hydrophobic and hydrophilic surfaces, and supply for the first time theoretical references for understanding the mechanics at the atomistic origins of macroscale ice adhesion.
Molecular Dynamics Study of Helicobacter pylori Urease.
Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M
2014-05-13
Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc.2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.
MOLECULAR DYNAMIC SIMULATION OF PEPTIDE POLYELECTROLYTES
I. M. Neelov
2014-07-01
Full Text Available The paper deals with investigation of the conformational properties of some charged homopolypeptides in dilute aqueous solutions by computer simulation. A method of molecular dynamics for the full-atomic models of polyaspartic acid and polylysine with explicit account of water and counter-ions is used for this purpose. For systems containing these polypeptides we calculated time trajectories and the size, shape, distribution functions and time correlation functions of inertia radius and the distances between the ends of peptide chains. We have also calculated the solvatation characteristics of considered polyelectrolytes. We have found out that polyaspartic acid in dilute aqueous solution has more compact structure and more spherical shape than polylysine. We have shown that these differences are due to different interaction between the polypeptides and water molecules (in particular, the quality and quantity of hydrogen bonds formed by these peptides with water, and the difference in an amount of ion pairs formed by the charged groups of the peptides and counter-ions. The obtained results should be taken into account for elaboration of new products based on the investigated peptides and their usage in various industrial and biomedical applications.
Molecular dynamics simulations of vibrated granular gases.
Barrat, Alain; Trizac, Emmanuel
2002-11-01
We present molecular dynamics simulations of monodisperse or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met experimentally, density and temperature fields display heterogeneous profiles in the direction perpendicular to the walls. A general equation of state for an arbitrary mixture of fluidized inelastic hard spheres is derived and successfully tested against numerical data. Single-particle velocity distribution functions with non-Gaussian features are also obtained, and the influence of various parameters (inelasticity coefficients, density, etc.) are analyzed. The validity of a recently proposed random restitution coefficient model is assessed through the study of projected collisions onto the direction perpendicular to that of energy injection. For the binary mixture, the nonequipartition of translational kinetic energy is studied and compared both to experimental data and to the case of homogeneous energy injection ("stochastic thermostat"). The rescaled velocity distribution functions are found to be very similar for both species.
Molecular dynamics simulation of flow in pores
Blömer, Jan
2001-08-01
The gaseous flow in nano-scale pores is of wide interest for many today's industrial applications, e.g., in microelectronics, nano-mechanical devices (Knudsen compressor) and reaction and adsorption at porous surfaces. This can be seen from a variety of papers of recent RGD Symposia. Furthermore it is possible to separate gases by porous membranes. Although the fundamental problem of all these applications is same, namely the important role of the gas-surface interaction in such small structures, we will primarily concentrate on the separation of different gas species by porous membranes. These membranes are typically very robust (temperature, chemical resistance) because they are made from ceramics which offers new application fields. Porous flow can roughly be divided in several flow regimes by the Knudsen number: From viscous flow to Knudsen diffusion to surface diffusion and up to capillary condensation. A Molecular Dynamics (MD) model for the gas as well as the surface is formulated to investigate the interaction of gas atoms or molecules with internal degrees of freedom and the pore. The MD method seems to be well suited to study these phenomena because it can deal with the high density and the many-body-interactions, which occur during the multilayer adsorption and condensation at the surface, although it is clear that it is limited to a small physical space because of its high computational consumption.
Direct anharmonic correction method by molecular dynamics
Liu, Zhong-Li; Li, Rui; Zhang, Xiu-Lu; Qu, Nuo; Cai, Ling-Cang
2017-04-01
The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties, the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI) method based on the temperature dependent phonon density of states (TD-PDOS) reduced from molecular dynamics simulations. Using the DFEI method, after anharmonic free energy corrections we reproduced the thermal expansion coefficients, the specific heat, the thermal pressure, the isothermal bulk modulus, and the Hugoniot P- V- T relationships of Cu easily and accurately. The extensive tests on other materials including metal, alloy, semiconductor and insulator also manifest that the DFEI method can easily uncover the rest anharmonicity that the quasi-harmonic approximation (QHA) omits. It is thus evidenced that the DFEI method is indeed a very efficient method used to conduct anharmonic effect corrections beyond QHA. More importantly it is much more straightforward and easier compared to previous anharmonic methods.
Efficient compression of molecular dynamics trajectory files.
Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James
2012-10-15
We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases.
Quantum molecular dynamics simulations of dense matter
Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)
1997-12-31
The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.
Debashis Mukherjee
2002-06-01
Full Text Available Abstract: We present in this paper two new versions of Rayleigh-SchrÃ‚Â¨odinger (RS and the Brillouin-Wigner (BW state-specific multi-reference perturbative theories (SSMRPT which stem from our state-specific multi-reference coupled-cluster formalism (SS-MRCC, developed with a complete active space (CAS. They are manifestly sizeextensive and are designed to avoid intruders. The combining coefficients cÃŽÂ¼ for the model functions ÃÂ†ÃŽÂ¼ are completely relaxed and are obtained by diagonalizing an effective operator in the model space, one root of which is the target eigenvalue of interest. By invoking suitable partitioning of the hamiltonian, very convenient perturbative versions of the formalism in both the RS and the BW forms are developed for the second order energy. The unperturbed hamiltonians for these theories can be chosen to be of both MÃÂ†ller-Plesset (MP and Epstein-Nesbet (EN type. However, we choose the corresponding Fock operator fÃŽÂ¼ for each model function ÃÂ†ÃŽÂ¼, whose diagonal elements are used to define the unperturbed hamiltonian in the MP partition. In the EN partition, we additionally include all the diagonal direct and exchange ladders. Our SS-MRPT thus utilizes a multi-partitioning strategy. Illustrative numerical applications are presented for potential energy surfaces (PES of the ground (1ÃŽÂ£+ and the first delta (1ÃŽÂ” states of CH+ which possess pronounced multi-reference character. Comparison of the results with the corresponding full CI values indicates the efficacy of our formalisms.
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari ' Aldo Moro' , Bari (Italy)
2011-01-07
Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
Polymer deformation in Brownian ratchets: theory and molecular dynamics simulations.
Kenward, Martin; Slater, Gary W
2008-11-01
We examine polymers in the presence of an applied asymmetric sawtooth (ratchet) potential which is periodically switched on and off, using molecular dynamics (MD) simulations with an explicit Lennard-Jones solvent. We show that the distribution of the center of mass for a polymer in a ratchet is relatively wide for potential well depths U0 on the order of several kBT. The application of the ratchet potential also deforms the polymer chains. With increasing U0 the Flory exponent varies from that for a free three-dimensional (3D) chain, nu=35 (U0=0), to that corresponding to a 2D compressed (pancake-shaped) polymer with a value of nu=34 for moderate U0. This has the added effect of decreasing a polymer's diffusion coefficient from its 3D value D3D to that of a pancaked-shaped polymer moving parallel to its minor axis D2D. The result is that a polymer then has a time-dependent diffusion coefficient D(t) during the ratchet off time. We further show that this suggests a different method to operate a ratchet, where the off time of the ratchet, toff, is defined in terms of the relaxation time of the polymer, tauR. We also derive a modified version of the Bader ratchet model [Bader, Proc. Natl. Acad. Sci. U.S.A. 96, 13165 (1999)] which accounts for this deformation and we present a simple expression to describe the time dependent diffusion coefficient D(t). Using this model we then illustrate that polymer deformation can be used to modulate polymer migration in a ratchet potential.
Fujisaki, Hiroshi; Hirao, Kimihiko; Straub, John E; Stock, Gerhard
2008-01-01
Employing extensive quantum-chemical calculations at the DFT/B3LYP and MP2 level, a quartic force field of isolated N-methylacetamide is constructed. Taking into account 24 vibrational degrees of freedom, the model is employed to perform numerically exact vibrational configuration interaction calculations of the vibrational energy relaxation of the amide I mode. It is found that the energy transfer pathways may sensitively depend on details of the theoretical description. Moreover, the exact reference calculations were used to study the applicability and accuracy of (i) the quasiclassical trajectory method, (ii) time-dependent second-order perturbation theory, and (iii) the instantaneous normal mode description of frequency fluctuations. Based on the results, several strategies to describe vibrational energy relaxation in biomolecular systems are discussed.
Relaxation of the entanglement spectrum in quench dynamics of topological systems
Jhu, Yi-Hao; Chen, Pochung; Chung, Ming-Chiang
2017-07-01
In this paper, we investigate how the entanglement spectrum relaxes to its steady-state values in one-dimensional quadratic systems after a quantum quench. In particular, we apply saddle-point expansion to dimerized chains and 1D p-wave superconductors. We found the entanglement spectrum to always exhibit a power-law relaxation superimposed with oscillations at certain characteristic angular frequencies. For dimerized chains, we found the exponent ν of the power-law decay to always be 3/2 . For 1D p-wave superconductors, however, we found that, depending on the initial and final Hamiltonian, the exponent ν can take its value from a limited list of values, the smallest possible of which is ν=1/2 , which leads to a very slow convergence to its steady-state value.
YANG Yanwu; WANG Dehua; QIU Jianqing; QIAN Baogong; WANG Hongzuo
1992-01-01
The carbon-13 spin-spin relaxation times of fluorine-containing ionomers are measured and motional correlation times τ0 and τd are calculated by using VJGM model. The results show that the motions of polymer main chain in ionomers become more difficult with increasing of ionization degree and contents of functional group, and depend on the fine structures and stability of ionic microdomains.
Structure and Dynamics of Polymers in Cylindrical Nanoconfinement: A Molecular Dynamics Study
Pressly, James; Riggleman, Robert; Winey, Karen
The structure and dynamics of polymers under nanoconfinement is critical for understanding how polymers behave in applications from hydraulic fracking to fabricating integrated circuits. We previously used simulations to explore the effect of the diameter of cylindrical pores (d = 10-40 σ, where σ is the unit length in reduced units) on polymer end-to-end distance (Ree,perp, Ree,par) , entanglement density, melt diffusion coefficient (D), and local relaxation time (τperp, τpar) at fixed polymer chain length (N = 350). These studies found D, Ree,par, and τperp increased with increasing confinement while entanglement density, Ree,perp, and τpar decreased. Experiments also found that D increased but to a lesser extent. Here, we examine the molecular weight dependence of these properties using N = 25, 50, 100, 200, 350, and 500 confined to pores of diameter 14 σ to examine a range of confinements. Our preliminary results show that as N increases D and Ree,par, increase as well, relative to the unconfined state, while entanglement density and Ree,perp decrease, consistent with our previous work. Interestingly, τ is shown to be independent of chain length indicating the impact of confinement imposed by reducing pore diameter is distinct from that imposed by increasing chain length.
Syryamina, V. N.; Dzuba, S. A.
2012-10-01
Electron paramagnetic resonance (EPR) spectroscopy in the form of pulsed electron-electron double resonance (ELDOR) was applied to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayers containing lipids that were spin-labeled at different carbon positions along the lipid acyl chain. Pulsed ELDOR detects motionally induced spin flips of nitrogen nuclei in the nitroxide spin labels, which manifests itself as magnetization transfer (MT) in the nitroxide EPR spectrum. The MT effect was observed over a wide temperature range (100-225 K) on a microsecond time scale. In line with a previous study on molecular glasses [N. P. Isaev and S. A. Dzuba, J. Chem. Phys. 135, 094508 (2011), 10.1063/1.3633241], the motions that induce MT effect were suggested to have the same nature as those in dielectric secondary (β) Johari-Goldstein fast relaxation. The results were compared with literature dielectric relaxation data for POPC bilayers, revealing some common features. Molecular motions resulting in MT are faster for deeper spin labels in the membrane interior. The addition of cholesterol to the bilayer suppresses the lipid motions near the steroid nucleus and accelerates the lipid motions beyond the steroid nucleus, in the bilayer interior. This finding was attributed to the lipid acyl chains being more ordered near the steroid nucleus and less ordered in the bilayer interior. The motions are absent in dry lipids, indicating that the motions are determined by intermolecular interactions in the bilayer.
Combined molecular dynamics-spin dynamics simulations of bcc iron
Perera, Meewanage Dilina N [ORNL; Yin, Junqi [ORNL; Landau, David P [University of Georgia, Athens, GA; Nicholson, Don M [ORNL; Stocks, George Malcolm [ORNL; Eisenbach, Markus [ORNL; Brown, Greg [ORNL
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.