NASA Astrophysics Data System (ADS)
Brennan, John K.; Lísal, Martin; Gubbins, Keith E.; Rice, Betsy M.
2004-12-01
A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2+3H2⇔2NH3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.
Bresme, F.; Armstrong, J.
2014-01-07
We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation.
NASA Astrophysics Data System (ADS)
Gunnerson, Kim N.; Brooksby, Craig; Prezhdo, Oleg V.; Reid, Philip J.
2007-10-01
The results of our earlier work [C. Brooksby, O. V. Prezhdo, and P. J. Reid, J. Chem. Phys. 119, 9111 (2003)] rationalizing the surprisingly weak solvent dependence of the dynamics following photoexcitation of chlorine dioxide in water, chloroform, and cyclohexane are thoroughly tested. Comparisons are made between equilibrium and nonequilibrium solvent response, equilibrium response in the ground and excited electronic states, as well as the cumulant and direct evaluation of the optical response function. In general, the linear response and cumulant approximations are found to hold, although minor deviations are found with all solvents. The ground state, linear response, and cumulant data show best agreement with experiment, most likely due to the better tested ground-state force field and the robust behavior of the linear response and cumulant approximations. The main conclusion of our earlier work explaining the weak solvent dependence by the domination of the van der Waals interaction component remains intact within the more advanced treatments. However, the molecular origin of this surprising experimental observation is different in water and chloroform compared to cyclohexane.
NASA Astrophysics Data System (ADS)
Masnoon, Ahmed Shafkat; Bipasha, Ferdaushi Alam; Morshed, A. K. M. M.
2016-07-01
The effect of nanoparticles decoration on the thermal conductivity of a nanowire is studied using Non Equilibrium Molecular Dynamics (NEMD) simulation. The simulation was conducted using simplified molecular model with Lennard-Jones potential. Argon-like solid was used as the material for both the nanowire and nanoparticles. Nanoparticles were placed on the surface of the nanowire and also embedded inside the structure. Non-equilibrium molecular dynamics simulation was conducted by imposing temperature gradient along the length of the nanowire and thermal conductivity of the nanowire was calculated. Nanowire without any nanoparticles was used as the baseline data. Due to presence of nanoparticles thermal conductivity of the nanowire was observed to decrease and up to 40% reduction in thermal conductivity was observed. With the increase in number of the nanoparticles, thermal conductivity was observed to decrease; however size of nanoparticles has little effect.
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
DePaul, Allison J.; Thompson, Erik J.; Patel, Sarav S.; Haldeman, Kristin; Sorin, Eric J.
2010-01-01
Conformational equilibrium within the ubiquitous GNRA tetraloop motif was simulated at the ensemble level, including 10 000 independent all-atom molecular dynamics trajectories totaling over 110 µs of simulation time. This robust sampling reveals a highly dynamic structure comprised of 15 conformational microstates. We assemble a Markov model that includes transitions ranging from the nanosecond to microsecond timescales and is dominated by six key loop conformations that contribute to fluctuations around the native state. Mining of the Protein Data Bank provides an abundance of structures in which GNRA tetraloops participate in tertiary contact formation. Most predominantly observed in the experimental data are interactions of the native loop structure within the minor groove of adjacent helical regions. Additionally, a second trend is observed in which the tetraloop assumes non-native conformations while participating in multiple tertiary contacts, in some cases involving multiple possible loop conformations. This tetraloop flexibility can act to counterbalance the energetic penalty associated with assuming non-native loop structures in forming tertiary contacts. The GNRA motif has thus evolved not only to readily participate in simple tertiary interactions involving native loop structure, but also to easily adapt tetraloop secondary conformation in order to participate in larger, more complex tertiary interactions. PMID:20223768
Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water
NASA Astrophysics Data System (ADS)
Bresme, Fernando
2001-10-01
Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water (CFM) [Lemberg and Stillinger, J. Chem. Phys. 62, 1677 (1975)] are presented. We consider a model based on a functional form introduced in theoretical studies of associating systems employing integral equations [F. Bresme, J. Chem. Phys. 108, 4505 (1998)]. Results on thermodynamic, dynamic, dielectric, and coexistence properties are presented. The central force model shows satisfactory agreement with the experimental results in all these cases. In addition, nonequilibrium molecular-dynamics simulations show that the CFM predicts a decrease of the thermal conductivity with temperature, as observed in the experiment, but this dependence is reproduced qualitatively at temperatures characteristic of supercooled states. These results emphasize the need for further studies of the heat conduction and properties of water in these conditions. Overall the present potential should provide a basis for further theoretical and simulation studies of complex systems where water is present.
NASA Astrophysics Data System (ADS)
Cartoixà, Xavier; Dettori, Riccardo; Melis, Claudio; Colombo, Luciano; Rurali, Riccardo
2016-07-01
We study thermal transport in porous Si nanowires (SiNWs) by means of approach-to-equilibrium molecular dynamics simulations. We show that the presence of pores greatly reduces the thermal conductivity, κ, of the SiNWs as long mean free path phonons are suppressed. We address explicitly the dependence of κ on different features of the pore topology—such as the porosity and the pore diameter—and on the nanowire (NW) geometry—diameter and length. We use the results of the molecular dynamics calculations to tune an effective model, which is capable of capturing the dependence of κ on porosity and NW diameter. The model illustrates the failure of Matthiessen's rule to describe the coupling between boundary and pore scattering, which we account for by the inclusion of an additional empirical term.
Symmetry-adapted non-equilibrium molecular dynamics of chiral carbon nanotubes under tensile loading
NASA Astrophysics Data System (ADS)
Aghaei, Amin; Dayal, Kaushik
2011-06-01
We report on non-equilibrium molecular dynamics calculations of chiral single-wall carbon nanotubes using the framework of Objective Structures. This enables us to adapt molecular dynamics to the symmetry of chiral nanotubes and efficiently simulate these systems with small unit cells. We outline the method and the adaptation of a conventional thermostat and barostat to this setting. We then apply the method in order to examine the behavior of nanotubes with various chiralities subject to a constant extensional strain rate. We examine the effects of temperature, strain rate, and pre-compression/pre-tension. We find a range of failure mechanisms, including the formation of Stone-Wales defects, the opening of voids, and the motion of atoms out of the cross-section.
NASA Astrophysics Data System (ADS)
English, Niall J.; Clarke, Elaine T.
2013-09-01
Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.
Equilibrium fractionation of H and O isotopes in water from path integral molecular dynamics
NASA Astrophysics Data System (ADS)
Pinilla, Carlos; Blanchard, Marc; Balan, Etienne; Ferlat, Guillaume; Vuilleumier, Rodolphe; Mauri, Francesco
2014-06-01
The equilibrium fractionation factor between two phases is of importance for the understanding of many planetary and environmental processes. Although thermodynamic equilibrium can be achieved between minerals at high temperature, many natural processes involve reactions between liquids or aqueous solutions and solids. For crystals, the fractionation factor α can be theoretically determined using a statistical thermodynamic approach based on the vibrational properties of the phases. These calculations are mostly performed in the harmonic approximation, using empirical or ab-initio force fields. In the case of aperiodic and dynamic systems such as liquids or solutions, similar calculations can be done using finite-size molecular clusters or snapshots obtained from molecular dynamics (MD) runs. It is however difficult to assess the effect of these approximate models on the isotopic fractionation properties. In this work we present a systematic study of the calculation of the D/H and 18O/16O equilibrium fractionation factors in water for the liquid/vapour and ice/vapour phases using several levels of theory within the simulations. Namely, we use a thermodynamic integration approach based on Path Integral MD calculations (PIMD) and an empirical potential model of water. Compared with standard MD, PIMD takes into account quantum effects in the thermodynamic modeling of systems and the exact fractionation factor for a given potential can be obtained. We compare these exact results with those of modeling strategies usually used, which involve the mapping of the quantum system on its harmonic counterpart. The results show the importance of including configurational disorder for the estimation of isotope fractionation in liquid phases. In addition, the convergence of the fractionation factor as a function of parameters such as the size of the simulated system and multiple isotope substitution is analyzed, showing that isotope fractionation is essentially a local effect in
Insight into lattice thermal impedance via equilibrium molecular dynamics: case study on Al
NASA Astrophysics Data System (ADS)
Evteev, Alexander V.; Levchenko, Elena V.; Momenzadeh, Leila; Belova, Irina V.; Murch, Graeme E.
2016-02-01
Using results of equilibrium molecular dynamics simulation in conjunction with the Green-Kubo formalism, we present a general treatment of thermal impedance of a crystal lattice with a monatomic unit cell. The treatment is based on an analytical expression for the heat current autocorrelation function which reveals, in a monatomic lattice, an energy gap between the origin of the phonon states and the beginning of the energy spectrum of the so-called acoustic short-range phonon modes. Although, we consider here the f.c.c. Al model as a case example, the analytical expression is shown to be consistent for different models of elemental f.c.c. crystals over a wide temperature range. Furthermore, we predict a frequency 'window' where the thermal waves can be generated in a monatomic lattice by an external periodic temperature perturbation.
A localized momentum constraint for non-equilibrium molecular dynamics simulations.
Smith, E R; Heyes, D M; Dini, D; Zaki, T A
2015-02-21
A method which controls momentum evolution in a sub-region within a molecular dynamics simulation is derived from Gauss's principle of least constraint. The technique for localization is founded on the equations by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] expressed in a weak form according to the control volume (CV) procedure derived by Smith et al. [Phys. Rev. E. 85, 056705 (2012)]. A term for the advection of molecules appears in the derived constraint and is shown to be essential in order to exactly control the time evolution of momentum in the subvolume. The numerical procedure converges the total momentum in the CV to the target value to within machine precision in an iterative manner. The localized momentum constraint can prescribe essentially arbitrary flow fields in non-equilibrium molecular dynamics simulations. The methodology also forms a rigorous mathematical framework for introducing coupling constraints at the boundary between continuum and discrete systems. This functionality is demonstrated with a boundary-driven flow test case. PMID:25702005
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.
Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations
Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki
2015-08-17
The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)
Gheribi, Aïmen E; Salanne, Mathieu; Chartrand, Patrice
2015-03-28
The composition dependence of thermal transport properties of the (Na,K)Cl rocksalt solid solution is investigated through equilibrium molecular dynamics (EMD) simulations in the entire range of composition and the results are compared with experiments published in recent work [Gheribi et al., J. Chem. phys. 141, 104508 (2014)]. The thermal diffusivity of the (Na,K)Cl solid solution has been measured from 473 K to 823 K using the laser flash technique, and the thermal conductivity was deduced from critically assessed data of heat capacity and density. The thermal conductivity was also predicted at 900 K in the entire range of composition by a series of EMD simulations in both NPT and NVT statistical ensembles using the Green-Kubo theory. The aim of the present paper is to provide an objective analysis of the capability of EMD simulations in predicting the composition dependence of the thermal transport properties of halide solid solutions. According to the Klemens-Callaway [P. G. Klemens, Phys. Rev. 119, 507 (1960) and J. Callaway and H. C. von Bayer, Phys. Rev. 120, 1149 (1960)] theory, the thermal conductivity degradation of the solid solution is explained by mass and strain field fluctuations upon the phonon scattering cross section. A rigorous analysis of the consistency between the theoretical approach and the EMD simulations is discussed in detail. PMID:25833567
Haxhimali, Tomorr; Rudd, Robert E; Cabot, William H; Graziani, Frank R
2015-11-01
We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 10^{25} ions/cc. The motion of 30,000-120,000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We systematically study different mixtures through a series of simulations with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. In the more strongly coupled plasmas, the kinetic theory does not agree well with the MD results. We develop a simple model that interpolates between classical kinetic theories at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated, ranging from moderately weakly coupled to moderately strongly coupled asymmetric plasma mixtures. PMID:26651805
NASA Astrophysics Data System (ADS)
Haxhimali, Tomorr; Rudd, Robert; Cabot, William; Graziani, Frank
2015-11-01
We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and Inertial Confinement Fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 1025 ions/cc. The motion of 30000-120000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We study different mixtures with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. We introduce a model that interpolates between a screened-plasma kinetic theory at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated. This work was performed under the auspices of the US Dept. of Energy by Lawrence Livermore National Security, LLC under Contract DE-AC52-07NA27344.
NASA Technical Reports Server (NTRS)
Haskins, Justin; Kinaci, Alper; Sevik, Cem; Cagin, Tahir
2012-01-01
It is widely known that graphene and many of its derivative nanostructures have exceedingly high reported thermal conductivities (up to 4000 W/mK at 300 K). Such attractive thermal properties beg the use of these structures in practical devices; however, to implement these materials while preserving transport quality, the influence of structure on thermal conductivity should be thoroughly understood. For graphene nanostructures, having average phonon mean free paths on the order of one micron, a primary concern is how size influences the potential for heat conduction. To investigate this, we employ a novel technique to evaluate the lattice thermal conductivity from the Green-Kubo relations and equilibrium molecular dynamics in systems where phonon-boundary scattering dominates heat flow. Specifically, the thermal conductivities of graphene nanoribbons and carbon nanotubes are calculated in sizes up to 3 microns, and the relative influence of boundary scattering on thermal transport is determined to be dominant at sizes less than 1 micron, after which the thermal transport largely depends on the quality of the nanostructure interface. The method is also extended to carbon nanostructures (fullerenes) where phonon confinement, as opposed to boundary scattering, dominates, and general trends related to the influence of curvature on thermal transport in these materials are discussed.
Non-equilibrium molecular dynamics simulation of the unstirred layer in the osmotically driven flow
NASA Astrophysics Data System (ADS)
Konno, Keito; Itano, Tomoaki; Seki, Masako
2015-11-01
We studied the solvent flows driven by the osmotic pressure difference across the semi-permeable membrane. The flow penetrating from the low concentration side transports away solutes adjacent of the membrane, so that the concentration is reduced significantly only at the vicinity of the membrane. It is expected that the relatively low solute concentration develops into a thin boundary layer in the vicinity of the membrane in the case of absence of external stirring process, which is termed as un-stirred layer (USL). To investigate concentration distribution in USL, we carried out non-equilibrium molecular dynamics simulations. The flows driven by th osmotic pressure are idealized as 2 dimensional hard disk model, which is composed of solvent and solute molecules. The membrane is modeled as a medium composed of stationary parallel rods distributed by a spatial interval, which is less than the diameter of the solute molecules. The following results were obtained from the numerical simulation. First, the thickness of USL, which was estimated from the obtained concentration distribution, is on the order of a length determined by mean free path. Second, USL was semicircle the center of which is on the end of pore of membrane.
NASA Astrophysics Data System (ADS)
Haxhimali, Tomorr; Rudd, Robert E.; Cabot, William H.; Graziani, Frank R.
2015-11-01
We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 1025 ions/cc. The motion of 30 000-120 000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We systematically study different mixtures through a series of simulations with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. In the more strongly coupled plasmas, the kinetic theory does not agree well with the MD results. We develop a simple model that interpolates between classical kinetic theories at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated, ranging from moderately weakly coupled to moderately strongly coupled asymmetric plasma mixtures.
Gheribi, Aïmen E; Chartrand, Patrice
2016-02-28
A theoretical model for the description of thermal conductivity of molten salt mixtures as a function of composition and temperature is presented. The model is derived by considering the classical kinetic theory and requires, for its parametrization, only information on thermal conductivity of pure compounds. In this sense, the model is predictive. For most molten salt mixtures, no experimental data on thermal conductivity are available in the literature. This is a hindrance for many industrial applications (in particular for thermal energy storage technologies) as well as an obvious barrier for the validation of the theoretical model. To alleviate this lack of data, a series of equilibrium molecular dynamics (EMD) simulations has been performed on several molten chloride systems in order to determine their thermal conductivity in the entire range of composition at two different temperatures: 1200 K and 1300 K. The EMD simulations are first principles type, as the potentials used to describe the interactions have been parametrized on the basis of first principle electronic structure calculations. In addition to the molten chlorides system, the model predictions are also compared to a recent similar EMD study on molten fluorides and with the few reliable experimental data available in the literature. The accuracy of the proposed model is within the reported numerical and/or experimental errors. PMID:26931711
Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics
NASA Astrophysics Data System (ADS)
Marcolongo, Aris; Umari, Paolo; Baroni, Stefano
2014-03-01
The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids.
Length dependence of thermal conductivity by approach-to-equilibrium molecular dynamics
NASA Astrophysics Data System (ADS)
Zaoui, Hayat; Palla, Pier Luca; Cleri, Fabrizio; Lampin, Evelyne
2016-08-01
The length dependence of thermal conductivity over more than two orders of magnitude has been systematically studied for a range of materials, interatomic potentials, and temperatures using the atomistic approach-to-equilibrium molecular dynamics (AEMD) method. By comparing the values of conductivity obtained for a given supercell length and maximum phonon mean free path (MFP), we find that such values are strongly correlated, demonstrating that the AEMD calculation with a supercell of finite length actually probes the thermal conductivity corresponding to a maximum phonon MFP. As a consequence, the less pronounced length dependence usually observed for poorer thermal conductors, such as amorphous silica, is physically justified by their shorter average phonon MFP. Finally, we compare different analytical extrapolations of the conductivity to infinite length and demonstrate that the frequently used Matthiessen rule is not applicable in AEMD. An alternative extrapolation more suitable for transient-time, finite-supercell simulations is derived. This approximation scheme can also be used to classify the quality of different interatomic potential models with respect to their capability of predicting the experimental thermal conductivity.
Gheribi, Aïmen E. Chartrand, Patrice; Salanne, Mathieu
2015-03-28
The composition dependence of thermal transport properties of the (Na,K)Cl rocksalt solid solution is investigated through equilibrium molecular dynamics (EMD) simulations in the entire range of composition and the results are compared with experiments published in recent work [Gheribi et al., J. Chem. phys. 141, 104508 (2014)]. The thermal diffusivity of the (Na,K)Cl solid solution has been measured from 473 K to 823 K using the laser flash technique, and the thermal conductivity was deduced from critically assessed data of heat capacity and density. The thermal conductivity was also predicted at 900 K in the entire range of composition by a series of EMD simulations in both NPT and NVT statistical ensembles using the Green-Kubo theory. The aim of the present paper is to provide an objective analysis of the capability of EMD simulations in predicting the composition dependence of the thermal transport properties of halide solid solutions. According to the Klemens-Callaway [P. G. Klemens, Phys. Rev. 119, 507 (1960) and J. Callaway and H. C. von Bayer, Phys. Rev. 120, 1149 (1960)] theory, the thermal conductivity degradation of the solid solution is explained by mass and strain field fluctuations upon the phonon scattering cross section. A rigorous analysis of the consistency between the theoretical approach and the EMD simulations is discussed in detail.
English, Niall J; Garate, José-A
2016-08-28
An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ∼0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region. PMID:27586951
NASA Astrophysics Data System (ADS)
Lemarchand, Claire A.; Bailey, Nicholas P.; Todd, Billy D.; Daivis, Peter J.; Hansen, Jesper S.
2015-06-01
The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed.
Zhang, Yong; Otani, Akihito; Maginn, Edward J
2015-08-11
Equilibrium molecular dynamics is often used in conjunction with a Green-Kubo integral of the pressure tensor autocorrelation function to compute the shear viscosity of fluids. This approach is computationally expensive and is subject to a large amount of variability because the plateau region of the Green-Kubo integral is difficult to identify unambiguously. Here, we propose a time decomposition approach for computing the shear viscosity using the Green-Kubo formalism. Instead of one long trajectory, multiple independent trajectories are run and the Green-Kubo relation is applied to each trajectory. The averaged running integral as a function of time is fit to a double-exponential function with a weighting function derived from the standard deviation of the running integrals. Such a weighting function minimizes the uncertainty of the estimated shear viscosity and provides an objective means of estimating the viscosity. While the formal Green-Kubo integral requires an integration to infinite time, we suggest an integration cutoff time tcut, which can be determined by the relative values of the running integral and the corresponding standard deviation. This approach for computing the shear viscosity can be easily automated and used in computational screening studies where human judgment and intervention in the data analysis are impractical. The method has been applied to the calculation of the shear viscosity of a relatively low-viscosity liquid, ethanol, and relatively high-viscosity ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethane-sulfonyl)imide ([BMIM][Tf2N]), over a range of temperatures. These test cases show that the method is robust and yields reproducible and reliable shear viscosity values. PMID:26574439
Vapor-liquid equilibrium of ethanol by molecular dynamics simulation and Voronoi tessellation.
Fern, Jared T; Keffer, David J; Steele, William V
2007-11-22
Explicit atom simulations of ethanol were performed by molecular dynamics using the OPLS-AA potential. The phase densities were determined self-consistently by comparing the distribution of Voronoi volumes from two-phase and single-phase simulations. This is the first demonstration of the use of Voronoi tessellation in two-phase molecular dynamics simulation of polyatomic fluids. This technique removes all arbitrary determination of the phase diagram by using single-phase simulations to self-consistently validate the probability distribution of Voronoi volumes of the liquid and vapor phases extracted from the two-phase molecular dynamics simulations. Properties from the two phase simulations include critical temperature, critical density, critical pressure, phase diagram, surface tension, and molecule orientation at the interface. The simulations were performed from 375 to 472 K. Also investigated were the vapor pressure and hydrogen bonding along the two phase envelope. The phase envelope agrees extremely well with literature values from GEMC at lower temperatures. The combined use of two-phase molecular dynamics simulation and Voronoi tessellation allows us to extend the phase diagram toward the critical point. PMID:17973521
NASA Astrophysics Data System (ADS)
Nilsen, Ian A.; Osborne, Derek G.; White, Aaron M.; Anna, Jessica M.; Kubarych, Kevin J.
2014-10-01
Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ˜3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C6H6Cr(CO)3, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of kBT. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 kBT above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy.
Nilsen, Ian A; Osborne, Derek G; White, Aaron M; Anna, Jessica M; Kubarych, Kevin J
2014-10-01
Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ∼3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C6H6Cr(CO)3, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of kBT. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 kBT above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy. PMID:25296812
NASA Astrophysics Data System (ADS)
Pinilla, Carlos; Blanchard, Marc; Balan, Etienne; Natarajan, Suresh K.; Vuilleumier, Rodolphe; Mauri, Francesco
2015-08-01
The theoretical determination of the isotopic fractionation between an aqueous solution and a mineral is of utmost importance in Earth sciences. While for crystals, it is well established that equilibrium isotopic fractionation factors can be calculated using a statistical thermodynamic approach based on the vibrational properties, several theoretical methods are currently used to model ions in aqueous solution. In this work, we present a systematic study to determine the reduced partition function ratio (β-factor) of aqueous Mg2+ using several levels of theory within the simulations. In particular, using an empirical force field, we compare and discuss the performance of the exact results obtained from path integral molecular dynamics (PIMD) simulations, with respect to the more traditional methods based on vibrational properties and the cluster approximation. The results show the importance of including configurational disorder for the estimation of the equilibrium isotope fractionation factor. We also show that using the vibrational frequencies computed from snapshots taken from equilibrated classical molecular dynamics represents a good approximation for the study of aqueous ions. Based on these conclusions, the β-factor of aqueous Mg2+ have been estimated from a Car-Parrinello molecular dynamics (CPMD) simulation with an ab initio force field, and combined with the β-factors of carbonate minerals (magnesite, dolomite, calcite and aragonite). Mg β-factor of Mg-bearing aragonite, calculated here for the first time, displays a lower value than the three other carbonate minerals. This is explained by a strong distortion of the cationic site leading to a decrease of the coordination number during Ca-Mg substitution. Overall, the equilibrium magnesium isotope fractionation factors between aqueous Mg2+ and carbonate minerals that derive from this methodological study support the previous theoretical results obtained from embedded cluster models.
Malolepsza, Edyta; Secor, Maxim; Keyes, Tom
2015-09-23
A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed for simulating first-order phase transitions. The properties of the isobaric gREM ensemble are discussed and a study is presented of the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. As a result, phase diagrams, critical parameters, and a law of corresponding states are obtained.
Małolepsza, Edyta; Secor, Maxim; Keyes, Tom
2015-10-22
A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed to simulate first-order phase transitions. The properties of the isobaric gREM ensemble are discussed, and a study is presented for the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. Phase diagrams, critical parameters, and a law of corresponding states are obtained. PMID:26398582
Shin, Hyun-Ho; Yoon, Woong-Sup
2008-07-01
An Adaptive-Spatial Decomposition parallel algorithm was developed to increase computation efficiency for molecular dynamics simulations of nano-fluids. Injection of a liquid argon jet with a scale of 17.6 molecular diameters was investigated. A solid annular platinum injector was also solved simultaneously with the liquid injectant by adopting a solid modeling technique which incorporates phantom atoms. The viscous heat was naturally discharged through the solids so the liquid boiling problem was avoided with no separate use of temperature controlling methods. Parametric investigations of injection speed, wall temperature, and injector length were made. A sudden pressure drop at the orifice exit causes flash boiling of the liquid departing the nozzle exit with strong evaporation on the surface of the liquids, while rendering a slender jet. The elevation of the injection speed and the wall temperature causes an activation of the surface evaporation concurrent with reduction in the jet breakup length and the drop size. PMID:19051924
Nilsen, Ian A.; Osborne, Derek G.; White, Aaron M.; Anna, Jessica M.; Kubarych, Kevin J.
2014-10-07
Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ∼3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C{sub 6}H{sub 6}Cr(CO){sub 3}, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of k{sub B}T. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 k{sub B}T above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy.
Equilibrium moisture content of a crosslinked epoxy network via molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Stoffels, M. T.; Staiger, M. P.; Bishop, C. M.
2016-06-01
This study presents molecular dynamics (MD) simulation methods for determining the solubility limit of water in a crosslinked epoxy network. Procedures are first presented for dynamically crosslinking an epoxy network consisting of diglycidyl ether bisphenol a (DGEBA) and isophorone diamine (IPD). Water molecules are then introduced into the crosslinked DGEBA-IPD structure. The excess chemical potential for the absorbed water was determined through combining thermodynamic integration and Widom’s test particle insertion methods. The limiting moisture uptake of the epoxy structure was determined through comparing the reduced chemical potential of the water held within the epoxy to that of pure water. The DGEBA-IPD epoxy system was found to have a moisture solubility of 3.50–3.75 wt.% when immersed in water at 300 K.
NASA Astrophysics Data System (ADS)
Sangiovanni, D. G.; Hellman, O.; Alling, B.; Abrikosov, I. A.
2016-03-01
We revisit the color-diffusion algorithm [Aeberhard et al., Phys. Rev. Lett. 108, 095901 (2012), 10.1103/PhysRevLett.108.095901] in non equilibrium ab initio molecular dynamics (NE-AIMD) and propose a simple efficient approach for the estimation of monovacancy jump rates in crystalline solids at temperatures well below melting. Color-diffusion applied to monovacancy migration entails that one lattice atom (colored atom) is accelerated toward the neighboring defect site by an external constant force F. Considering bcc molybdenum between 1000 and 2800 K as a model system, NE-AIMD results show that the colored-atom jump rate kNE increases exponentially with the force intensity F , up to F values far beyond the linear-fitting regime employed previously. Using a simple model, we derive an analytical expression which reproduces the observed kNE(F ) dependence on F . Equilibrium rates extrapolated by NE-AIMD results are in excellent agreement with those of unconstrained dynamics. The gain in computational efficiency achieved with our approach increases rapidly with decreasing temperatures and reaches a factor of 4 orders of magnitude at the lowest temperature considered in the present study.
Frentrup, Hendrik; Hart, Kyle E.; Colina, Coray M.; Müller, Erich A.
2015-01-01
We study the permeation dynamics of helium and carbon dioxide through an atomistically detailed model of a polymer of intrinsic microporosity, PIM-1, via non-equilibrium molecular dynamics (NEMD) simulations. This work presents the first explicit molecular modeling of gas permeation through a high free-volume polymer sample, and it demonstrates how permeability and solubility can be obtained coherently from a single simulation. Solubilities in particular can be obtained to a very high degree of confidence and within experimental inaccuracies. Furthermore, the simulations make it possible to obtain very specific information on the diffusion dynamics of penetrant molecules and yield detailed maps of gas occupancy, which are akin to a digital tomographic scan of the polymer network. In addition to determining permeability and solubility directly from NEMD simulations, the results shed light on the permeation mechanism of the penetrant gases, suggesting that the relative openness of the microporous topology promotes the anomalous diffusion of penetrant gases, which entails a deviation from the pore hopping mechanism usually observed in gas diffusion in polymers. PMID:25764366
Molecular dynamics study of nanobubbles in the equilibrium Lennard-Jones fluid.
Zhukhovitskii, D I
2013-10-28
We employ a model, in which the density fluctuations in a bulk liquid are represented as presence of the clusters of molecules with the lowered number of nearest neighbors (number of bonds). The nanobubble size distribution is calculated on the basis of a close analogy between the surface part of the work of formation for a cluster and for a nanobubble. The pre-exponential factor for this distribution is related to the fluid compressibility. Estimates made for different liquids show that it can be noticeably different from that adopted in the classical nucleation theory (CNT). Molecular dynamics (MD) simulation is performed for a liquid inside a macroscopic droplet of molecules interacting via the Lennard-Jones potential plus a long-range tail. The nanobubbles are identified by clusters of bond-deficient particles with the optimum number of bonds that provide the maximum nanobubble number density and maximum resolvable nanobubble equimolar size. The results of MD simulation are in qualitatively better agreement with proposed theory than with CNT. PMID:24182055
Molecular dynamics study of nanobubbles in the equilibrium Lennard-Jones fluid
NASA Astrophysics Data System (ADS)
Zhukhovitskii, D. I.
2013-10-01
We employ a model, in which the density fluctuations in a bulk liquid are represented as presence of the clusters of molecules with the lowered number of nearest neighbors (number of bonds). The nanobubble size distribution is calculated on the basis of a close analogy between the surface part of the work of formation for a cluster and for a nanobubble. The pre-exponential factor for this distribution is related to the fluid compressibility. Estimates made for different liquids show that it can be noticeably different from that adopted in the classical nucleation theory (CNT). Molecular dynamics (MD) simulation is performed for a liquid inside a macroscopic droplet of molecules interacting via the Lennard-Jones potential plus a long-range tail. The nanobubbles are identified by clusters of bond-deficient particles with the optimum number of bonds that provide the maximum nanobubble number density and maximum resolvable nanobubble equimolar size. The results of MD simulation are in qualitatively better agreement with proposed theory than with CNT.
NASA Astrophysics Data System (ADS)
Shim, Y.; Choi, M. Y.; Kim, Hyung J.
2005-01-01
Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe solutes. It is found that electrostriction plays an important role in both solvation structure and free energetics. The angular and radial distributions of cations and anions become more structured and their densities near the solute become enhanced as the solute charge separation grows. Due to the enhancement in structural rigidity induced by electrostriction, the force constant associated with solvent configuration fluctuations relevant to charge shift and transfer processes is also found to increase. The effective polarity and reorganization free energies of these ionic liquids are analyzed and compared with those of highly polar acetonitrile. Their screening behavior of electric charges is also investigated.
Pabón, Germán; Amzel, L. Mario
2006-01-01
We have studied the unfolding by force of one of the immunoglobulin domains of the muscle protein titin using molecular dynamics simulations at 300 K. Previous studies, done at constant pulling rates, showed that under the effect of the force two strands connected to each other by six backbone H-bonds are pulled apart. No details about the mechanism of H-bond breaking were provided. Our simulation protocol “pull and wait” was designed to correspond to very slow pulling, more similar to the rates used in experiments than are the protocols used in previous computational studies. Under these conditions interstrand backbone H-bonds are not “ripped apart” by the application of the force. Instead, small elongations produced by the force weaken specific backbone H-bonds with respect to water-backbone H-bonds. These weakened bonds allow a single water molecule to make H-bonds to the CO and the NH of the same backbone H-bond while they are still bound to each other. The backbone H-bond then breaks (distance >3.6 Å), but its donor and acceptor atoms remain bound to the same water molecule. Further separation of the chains takes place when a second water molecule makes an H-bond with either the protein backbone donor or acceptor atom. Thus, the force does not directly break the main chain H-bonds: it destabilizes them in such a way that they are replaced by H-bonds to water. With this mechanism, the force necessary to break all the H-bonds required to separate the two strands will be strongly dependent on the pulling speed. Further simulations carried out at low forces but long waiting times (≥ 500 ps, ≤ 10 ns) show that, given enough time, even a very small pulling force (<400 pN) is sufficient to destabilize the interstrand H-bonds and allow them to be replaced by H-bonds to two water molecules. As expected, increasing the temperature to 350 K allows the interstrand H-bonds to break at lower forces than those required at 300 K. PMID:16632514
NASA Technical Reports Server (NTRS)
Benjamin, Ilan; Pohorille, Andrew
1993-01-01
The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.
Phonon thermal transport outside of local equilibrium in nanowires via molecular dynamics
Zhou Ya; Strachan, Alejandro
2013-03-28
We study thermal transport through Pt nanowires that bridge planar contacts as a function of wire length and vibrational frequency of the contacts. When phonons in the contacts have lower average frequencies than those in the wires thermal transport occurs under conditions away from local equilibrium with low-frequency phonons experiencing a higher thermal gradient than high-frequency ones. This results in a size-dependent increase in the effective thermal conductivity of the wire with decreasing vibrational frequencies of the contacts. The interfacial resistivity when heat flows from the wire to the contact is also size-dependent and has the same physical origin in the lack of full equilibration in short nanowires. We develop a model based on a 1D atomic chain that captures the salient physics of the MD results.
NASA Astrophysics Data System (ADS)
Wang, Guan M.; Sandberg, William C.
2007-04-01
In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated
Ghatage, Dhairyashil; Tomar, Gaurav Shukla, Ratnesh K.
2015-03-28
Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.
Guo, Dezhou; Zybin, Sergey V; An, Qi; Goddard, William A; Huang, Fenglei
2016-01-21
The combustion or detonation of reacting materials at high temperature and pressure can be characterized by the Chapman-Jouguet (CJ) state that describes the chemical equilibrium of the products at the end of the reaction zone of the detonation wave for sustained detonation. This provides the critical properties and product kinetics for input to macroscale continuum simulations of energetic materials. We propose the ReaxFF Reactive Dynamics to CJ point protocol (Rx2CJ) for predicting the CJ state parameters, providing the means to predict the performance of new materials prior to synthesis and characterization, allowing the simulation based design to be done in silico. Our Rx2CJ method is based on atomistic reactive molecular dynamics (RMD) using the QM-derived ReaxFF force field. We validate this method here by predicting the CJ point and detonation products for three typical energetic materials. We find good agreement between the predicted and experimental detonation velocities, indicating that this method can reliably predict the CJ state using modest levels of computation. PMID:26688211
NASA Astrophysics Data System (ADS)
Ghatage, Dhairyashil; Tomar, Gaurav; Shukla, Ratnesh K.
2015-03-01
Non-equilibrium molecular dynamics (MD) simulations require imposition of non-periodic boundary conditions (NPBCs) that seamlessly account for the effect of the truncated bulk region on the simulated MD region. Standard implementation of specular boundary conditions in such simulations results in spurious density and force fluctuations near the domain boundary and is therefore inappropriate for coupled atomistic-continuum calculations. In this work, we present a novel NPBC model that relies on boundary atoms attached to a simple cubic lattice with soft springs to account for interactions from particles which would have been present in an untruncated full domain treatment. We show that the proposed model suppresses the unphysical fluctuations in the density to less than 1% of the mean while simultaneously eliminating spurious oscillations in both mean and boundary forces. The model allows for an effective coupling of atomistic and continuum solvers as demonstrated through multiscale simulation of boundary driven singular flow in a cavity. The geometric flexibility of the model enables straightforward extension to nonplanar complex domains without any adverse effects on dynamic properties such as the diffusion coefficient.
Frolov, T; Asta, M
2012-12-01
In this work a method is proposed for computing step free energies for faceted solid-liquid interfaces based on atomistic simulations. The method is demonstrated in an application to (111) interfaces in elemental Si, modeled with the classical Stillinger-Weber potential. The approach makes use of an adiabatic trapping procedure, and involves simulations of systems with coexisting solid and liquid phases separated by faceted interfaces containing islands with different sizes, for which the corresponding equilibrium temperatures are computed. We demonstrate that the calculated coexistence temperature is strongly affected by the geometry of the interface. We find that island radius is inversely proportional to superheating, allowing us to compute the step free energy by fitting simulation data within the formalism of classical nucleation theory. The step free energy value is computed to be γ(st) = 0.103 ± 0.005 × 10(-10) J/m. The approach outlined in this work paves the way to the calculation of step free energies relevant to the solidification of faceted crystals from liquid mixtures, as encountered in nanowire growth by the vapor-liquid-solid mechanism and in alloy casting. The present work also shows that at low undercoolings the Stillinger-Weber interatomic potential for Si tends to crystallize in the wurtzite, rather than the diamond-cubic structure. PMID:23231218
Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation
Schnell, Sondre K.; Skorpa, Ragnhild; Bedeaux, Dick; Kjelstrup, Signe; Vlugt, Thijs J. H.; Simon, Jean-Marc
2014-10-14
We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtained with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation.
Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Schnell, Sondre K.; Skorpa, Ragnhild; Bedeaux, Dick; Kjelstrup, Signe; Vlugt, Thijs J. H.; Simon, Jean-Marc
2014-10-01
We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtained with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation.
NASA Astrophysics Data System (ADS)
Chialvo, Ariel A.; Debenedetti, Pablo G.
1991-04-01
To date, the calculation of shear viscosity for soft-core fluids via equilibrium molecular dynamics has been done almost exclusively using the Green-Kubo formalism. The alternative mean-squared displacement approach has not been used, except for hard-sphere fluids, in which case the expression proposed by Helfand [Phys. Rev. 119, 1 (1960)] has invariably been selected. When written in the form given by McQuarrie [Statistical Mechanics (Harper & Row, New York, 1976), Chap. 21], however, the mean-squared displacement approach offers significant computational advantages over both its Green-Kubo and Helfand counterparts. In order to achieve comparable statistical significance, the number of experiments needed when using the Green-Kubo or Helfand formalisms is more than an order of magnitude higher than for the McQuarrie expression. For pairwise-additive systems with zero linear momentum, the McQuarrie method yields frame-independent shear viscosities. The hitherto unexplored McQuarrie implementation of the mean-squared displacement approach to shear-viscosity calculation thus appears superior to alternative methods currently in use.
NASA Astrophysics Data System (ADS)
Möller, Dietmar; Fischer, Johann
In order to determine the vapour liquid equilibrium of a pure fluid, the liquid and the vapour branch of the isotherms in the chemical potential μ vs pressure p-diagram, are constructed explicitly. The liquid branch is obtained by molecular dynamics simulations in an NpT-ensemble into which test particles are inserted to calculate the chemical potential. The vapour branch is obtained at lower temperatures by using the second virial coefficient, at higher temperatures it is determined again by simulations. As an example the two-centre Lennard-Jones fluid with elongation L = 0·505 is considered at temperatures ranging from 0·69 to 0·92 of the estimated critical temperature. As expected, the inaccuracies of the liquid chemical potential increase with decreasing temperature as a consequence of the increasing saturated density. The uncertainties in μ/RT range from 0·02 at the highest to 0·10 at the lowest temperature which creates an uncertainty in the reduced vapour pressure Pσ3/ɛ of the order of 0·002. Within that uncertainty, the vapour pressures agree with those obtained previously from perturbation theory. The saturated liquid densities agree within 2 per cent which is consistent with a previous comparison between perturbation theory and experimental results for fluorine. Finally, we note that all simulations were performed with vectorized codes on a CYBER 205.
NASA Astrophysics Data System (ADS)
Alaghemandi, Mohammad; Müller-Plathe, Florian; Böhm, Michael C.
2011-11-01
The thermal conductivity of composites of carbon nanotubes and polyamide-6,6 has been investigated using reverse non-equilibrium molecular dynamics simulations in a full atomistic resolution. It is found, in line with experiments, that the composites have thermal conductivities, which are only moderately larger than that of pure polyamide. The composite conductivities are orders of magnitude less than what would be expected from naïve additivity arguments. This means that the intrinsic thermal conductivities of isolated nanotubes, which exceed the best-conducting metals, cannot be harnessed for heat transport, when the nanotubes are embedded in a polymer matrix. The main reason is the high interfacial thermal resistance between the nanotubes and the polymer, which was calculated in addition to the total composite thermal conductivity as well as that of the subsystem. It hinders heat to be transferred from the slow-conducting polymer into the fast-conducting nanotubes and back into the polymer. This interpretation is in line with the majority of recent simulation works. An alternative explanation, namely, the damping of the long-wavelength phonons in nanotubes by the polymer matrix is not supported by the present calculations. These modes provide most of the polymers heat conduction. An additional minor effect is caused by the anisotropic structure of the polymer phase induced by the nearby nanotube surfaces. The thermal conductivity of the polymer matrix increases slightly in the direction parallel to the nanotubes, whereas it decreases perpendicular to it.
DYNAMIC EQUILIBRIUM IN THERAPEUTIC SITUATIONS.
ERIC Educational Resources Information Center
CARROLL, EDWARD J.
THE CONCEPT OF DYNAMIC EQUILIBRIUM IS USED TO EXAMINE THE OCCURRENCE OF CHANGE IN A THERAPEUTIC INTERVIEW AND TO PROPOSE A THEORY OF THERAPY. BY ANALYZING THE WORKINGS OF THE PSYCHOSOCIAL SYSTEM THROUGH THE GENERAL SYSTEMS THEORY, IT IS POSSIBLE TO SEE HOW CHANGE OCCURS IN AN INDIVIDUAL FAMILY OR COMMUNITY. APPLIED TO A FAMILY INTERVIEW, THE MODEL…
Jolley, Kenny; Gill, Simon P.A.
2009-10-20
A method for controlling the thermal boundary conditions of non-equilibrium molecular dynamics simulations is presented. The method is simple to implement into a conventional molecular dynamics code and independent of the atomistic model employed. It works by regulating the temperature in a thermostatted boundary region by feedback control to achieve the desired temperature at the edge of an inner region where the true atomistic dynamics are retained. This is necessary to avoid intrinsic boundary effects in non-equilibrium molecular dynamics simulations. Three thermostats are investigated: the global deterministic Nose-Hoover thermostat and two local stochastic thermostats, Langevin and stadium damping. The latter thermostat is introduced to avoid the adverse reflection of phonons that occurs at an abrupt interface. The method is then extended to allow atomistic/continuum models to be thermally coupled concurrently for the analysis of large steady state and transient heat conduction problems. The effectiveness of the algorithm is demonstrated for the example of heat flow down a three-dimensional atomistic rod of uniform cross-section subjected to a variety of boundary conditions.
NASA Astrophysics Data System (ADS)
Allen, Michael P.; Brown, David; Masters, Andrew J.
1994-03-01
In a recent paper, Chialvo and Debenedetti [Phys. Rev. A 43, 4289 (1991)] consider single-particle and collective expressions due, respectively, to McQuarrie [Statistical Mechanics (Harper and Row, New York, 1976)] and Helfand [Phys. Rev. 119, 1 (1960)] for the calculation of shear viscosities in molecular-dynamics simulations. We point out an error in the discussion of origin independence in this paper, and show that the prescriptions set out in it are not related to the shear viscosity.
Dang, L.X.
1999-05-01
Extensive molecular dynamics simulations are carried out to study the molecular interactions, liquid states, and liquid/vapor properties of dichloromethane. The study is also extended to the equilibrium properties of the liquid/liquid interface of water-dichloromethane. The intermolecular interactions among water, dichloromethane, and water-dichloromethane are described using our polarizable potential models. The equilibrium properties of liquid dichloromethane, including the radial distribution functions, the intermolecular structural factor, the self-diffusion coefficient, and the dielectric constant, are evaluated. The dielectric constant is computed using Ewald summation techniques and the computed result compared reasonably well with the available experimental data. Properties such as surface tensions and density profiles of liquid/vapor dichloromethane are evaluated. We found that the computed surface tensions for several temperatures are in excellent agreement with experimental data. The computed density profile of the liquid/liquid interface of water-dichloromethane is averaged over 1 ns and we found the computed profile to be quite smooth and stable. The effect of polarization on the liquid/liquid interfacial equilibrium properties is evaluated by computing the dipole moments of water and dichloromethane molecules as a function of the distance normal to the interface. We found that these values deviated significantly from the simulations that are based on nonpolarizable potential models. We attribute these observations to the changes in the electric fields around the water and dichloromethane molecules near the interface. {copyright} {ital 1999 American Institute of Physics.}
NASA Astrophysics Data System (ADS)
Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I.; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K.
2013-01-01
The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.
Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K
2013-01-21
The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses. PMID:23343292
Burnham, Christian J; English, Niall J
2016-04-28
Equilibrium molecular-dynamics (MD) simulations have been performed on metastable sI and sII polymorphs of empty hydrate lattices, in addition to liquid water and ice Ih. The non-polarisable TIP4P-2005, simple point charge model (SPC), and polarisable Thole-type models (TTM): TTM2, TTM3, and TTM4 water models were used in order to survey the differences between models and to see what differences can be expected when polarisability is incorporated. Rigid and flexible variants were used of each model to gauge the effects of flexibility. Power spectra are calculated and compared to density-of-states spectra inferred from inelastic neutron scattering (INS) measurements. Thermodynamic properties were also calculated, as well as molecular-dipole distributions. It was concluded that TTM models offer optimal fidelity vis-à-vis INS spectra, together with thermodynamic properties, with the flexible TTM2 model offering optimal placement of vibrational modes. PMID:27131553
NASA Astrophysics Data System (ADS)
Burnham, Christian J.; English, Niall J.
2016-04-01
Equilibrium molecular-dynamics (MD) simulations have been performed on metastable sI and sII polymorphs of empty hydrate lattices, in addition to liquid water and ice Ih. The non-polarisable TIP4P-2005, simple point charge model (SPC), and polarisable Thole-type models (TTM): TTM2, TTM3, and TTM4 water models were used in order to survey the differences between models and to see what differences can be expected when polarisability is incorporated. Rigid and flexible variants were used of each model to gauge the effects of flexibility. Power spectra are calculated and compared to density-of-states spectra inferred from inelastic neutron scattering (INS) measurements. Thermodynamic properties were also calculated, as well as molecular-dipole distributions. It was concluded that TTM models offer optimal fidelity vis-à-vis INS spectra, together with thermodynamic properties, with the flexible TTM2 model offering optimal placement of vibrational modes.
Non-equilibrium Dynamics of DNA Nanotubes
NASA Astrophysics Data System (ADS)
Hariadi, Rizal Fajar
Can the fundamental processes that underlie molecular biology be understood and simulated by DNA nanotechnology? The early development of DNA nanotechnology by Ned Seeman was driven by the desire to find a solution to the protein crystallization problem. Much of the later development of the field was also driven by envisioned applications in computing and nanofabrication. While the DNA nanotechnology community has assembled a versatile tool kit with which DNA nanostructures of considerable complexity can be assembled, the application of this tool kit to other areas of science and technology is still in its infancy. This dissertation reports on the construction of non-equilibrium DNA nanotube dynamic to probe molecular processes in the areas of hydrodynamics and cytoskeletal behavior. As the first example, we used DNA nanotubes as a molecular probe for elongational flow measurement in different micro-scale flow settings. The hydrodynamic flow in the vicinity of simple geometrical objects, such as a rigid DNA nanotube, is amenable to rigorous theoretical investigation. We measured the distribution of elongational flows produced in progressively more complex settings, ranging from the vicinity of an orifice in a microfluidic chamber to within a bursting bubble of Pacific ocean water. This information can be used to constrain theories on the origin of life in which replication involves a hydrodynamically driven fission process, such as the coacervate fission proposed by Oparin. A second theme of this dissertation is the bottom-up construction of a de novo artificial cytoskeleton with DNA nanotubes. The work reported here encompasses structural, locomotion, and control aspects of non-equilibrium cytoskeletal behavior. We first measured the kinetic parameters of DNA nanotube assembly and tested the accuracy of the existing polymerization models in the literature. Toward recapitulation of non-equilibrium cytoskeletal dynamics, we coupled the polymerization of DNA
NASA Astrophysics Data System (ADS)
Allen, Michael P.
1994-10-01
In a recent paper, Chialvo, Cummings, and Evans [Phys. Rev. E 47, 1702 (1993)] attempt to relate single-particle and collective expressions, due, respectively, to McQuarrie [Statistical Mechanics (Harper and Row, New York, 1976)] and Helfand [Phys. Rev. 119, 1 (1960)] for the calculation of shear viscosities in molecular dynamics simulations. We point out that their analysis does not correspond to the simulation algorithm they actually use, that the system-size dependence they derive and the extrapolation procedure they propose are incorrect, and that they have established no relation between their analysis and the shear viscosity. Our own analysis explains the simulation results in terms of the artificial way that periodic box boundary crossings are handled. We find no support for a link between the McQuarrie formula and any valid statistical mechanical expression for the shear viscosity.
NASA Astrophysics Data System (ADS)
Tseng, Huan-Chang; Wu, Jiann-Shing; Chang, Rong-Yeu
2008-07-01
Equilibrium and nonequilibrium molecular dynamics (MD) simulations have been performed in both isochoric-isothermal (NVT) and isobaric-isothermal (NPT) ensemble systems. Under steady state shearing conditions, thermodynamic states and rheological properties of liquid n-hexadecane molecules have been studied. Between equilibrium and nonequilibrium states, it is important to understand how shear rates (γ˙) affect the thermodynamic state variables of temperature, pressure, and density. At lower shear rates of γ˙<1×1011s-1, the relationships between the thermodynamic variables at nonequilibrium states closely approximate those at equilibrium states, namely, the liquid is very near its Newtonian fluid regime. Conversely, at extreme shear rates of γ˙>1×1011s-1, specific behavior of shear dilatancy is observed in the variations of nonequilibrium thermodynamic states. Significantly, by analyzing the effects of changes in temperature, pressure, and density on shear flow system, we report a variety of rheological properties including the shear thinning relationship between viscosity and shear rate, zero-shear-rate viscosity, rotational relaxation time, and critical shear rate. In addition, the flow activation energy and the pressure-viscosity coefficient determined through Arrhenius and Barus equations acceptably agree with the related experimental and MD simulation results.
Oderji, Hassan Yousefi; Ding, Hongbin; Behnejad, Hassan
2011-06-01
The second self-diffusion and viscosity virial coefficients of the Lennard-Jones (LJ) fluid were calculated by a detailed evaluation of the velocity and shear-stress autocorrelation functions using equilibrium molecular dynamics simulations at low and moderate densities. Accurate calculation of these coefficients requires corresponding transport coefficient values with low degrees of uncertainty. These were obtained via very long simulations by increasing the number of particles and by using the knowledge of correlation functions in the Green-Kubo method in conjunction with their corresponding generalized Einstein relations. The values of the self-diffusion and shear viscosity coefficients have been evaluated for systems with reduced densities between 0.0005 and 0.05 and reduced temperatures from 0.7 to 30.0. This provides a new insight into the transport coefficients beyond what can be offered by the Rainwater-Friend theory, which has not been developed for the self-diffusion coefficient. PMID:21797351
Tanaka, Kouichi; Ogata, Shuji; Kobayashi, Ryo; Tamura, Tomoyuki; Kitsunezuka, Masashi; Shinma, Atsushi
2013-11-21
Developing a composite material of polymers and micrometer-sized fillers with higher heat conductance is crucial to realize modular packaging of electronic components at higher densities. Enhancement mechanisms of the heat conductance of the polymer-filler interfaces by adding the surface-coupling agent in such a polymer composite material are investigated through the non-equilibrium molecular dynamics (MD) simulation. A simulation system is composed of α-alumina as the filler, bisphenol-A epoxy molecules as the polymers, and model molecules for the surface-coupling agent. The inter-atomic potential between the α-alumina and surface-coupling molecule, which is essential in the present MD simulation, is constructed to reproduce the calculated energies with the electronic density-functional theory. Through the non-equilibrium MD simulation runs, we find that the thermal resistance at the interface decreases significantly by increasing either number or lengths of the surface-coupling molecules and that the effective thermal conductivity of the system approaches to the theoretical value corresponding to zero thermal-resistance at the interface. Detailed analyses about the atomic configurations and local temperatures around the interface are performed to identify heat-transfer routes through the interface.
Equilibrium Molecular Thermodynamics from Kirkwood Sampling
2015-01-01
We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys.2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide. PMID:25915525
Open boundary molecular dynamics
NASA Astrophysics Data System (ADS)
Delgado-Buscalioni, R.; Sablić, J.; Praprotnik, M.
2015-09-01
This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.
Instability of quantum equilibrium in Bohm's dynamics
Colin, Samuel; Valentini, Antony
2014-01-01
We consider Bohm's second-order dynamics for arbitrary initial conditions in phase space. In principle, Bohm's dynamics allows for ‘extended’ non-equilibrium, with initial momenta not equal to the gradient of phase of the wave function (as well as initial positions whose distribution departs from the Born rule). We show that extended non-equilibrium does not relax in general and is in fact unstable. This is in sharp contrast with de Broglie's first-order dynamics, for which non-standard momenta are not allowed and which shows an efficient relaxation to the Born rule for positions. On this basis, we argue that, while de Broglie's dynamics is a tenable physical theory, Bohm's dynamics is not. In a world governed by Bohm's dynamics, there would be no reason to expect to see an effective quantum theory today (even approximately), in contradiction with observation. PMID:25383020
Lee, Seung G; Brunello, Giuseppe F; Jang, Seung S; Bucknall, David G
2009-10-01
Poly (N-vinyl-2-pyrrolidone-co-2-hydroxyethyl methacrylate) (P(VP-co-HEMA)) hydrogel system with a composition of VP:HEMA=37:13 was studied using molecular dynamics simulations in order to investigate the effect of the water content on the equilibrium structures and the mechanical properties. The degree of randomness of the monomer sequence for the random and the blocky copolymers, were 1.170 and 0.104, respectively, and the degree of polymerization was fixed at 50. The equilibrated density of the hydrogel was found to be larger for the random sequence than for the blocky sequence at low water contents (<40 wt%), but this density difference decreased with increasing water content. The pair correlation function analysis shows that VP is more hydrophilic than HEMA and that the random sequence hydrogel is solvated more than the blocky sequence hydrogel at low water content, which disappears with increasing water content. Correspondingly, the water structure is more disrupted by the random sequence hydrogel at low water content but eventually develops the expected bulk water-like structure with increasing water content. From mechanical deformation simulations, stress-strain analysis showed that the VP is found to relax more efficiently, especially in the blocky sequence, so that the blocky sequence hydrogel shows less stress levels compared to the random sequence hydrogel. As the water content increases, the stress level becomes identical for both sequences. The elastic moduli of the hydrogels calculated from the constant strain energy minimization show the same trend with the stress-strain analysis. PMID:19656562
Interactive molecular dynamics
NASA Astrophysics Data System (ADS)
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.
Dynamically defined measures and equilibrium states
NASA Astrophysics Data System (ADS)
Werner, Ivan
2011-12-01
A technique of dynamically defined measures is developed and its relation to the theory of equilibrium states is shown. The technique uses Carathéodory's method and the outer measure introduced in a previous work by I. Werner [Math. Proc. Camb. Phil. Soc. 140(2), 333-347 (2006), 10.1017/S0305004105009072]. As an application, equilibrium states for contractive Markov systems [I. Werner, J. London Math. Soc. 71(1), 236-258 (2005), 10.1112/S0024610704006088] are obtained.
ERIC Educational Resources Information Center
Silverberg, Lee J.; Raff, Lionel M.
2015-01-01
Thermodynamic spontaneity-equilibrium criteria require that in a single-reaction system, reactions in either the forward or reverse direction at equilibrium be nonspontaneous. Conversely, the concept of dynamic equilibrium holds that forward and reverse reactions both occur at equal rates at equilibrium to the extent allowed by kinetic…
Dynamical topological order parameters far from equilibrium
NASA Astrophysics Data System (ADS)
Budich, Jan Carl; Heyl, Markus
2016-02-01
We introduce a topological quantum number—coined dynamical topological order parameter (DTOP)—that is dynamically defined in the real-time evolution of a quantum many-body system and represented by a momentum space winding number of the Pancharatnam geometric phase. Our construction goes conceptually beyond the standard notion of topological invariants characterizing the wave function of a system, which are constants of motion under coherent time evolution. In particular, we show that the DTOP can change its integer value at discrete times where so called dynamical quantum phase transitions occur, thus serving as a dynamical analog of an order parameter. Interestingly, studying quantum quenches in one-dimensional two-banded Bogoliubov-de Gennes models, we find that the DTOP is capable of resolving if the topology of the system Hamiltonian has changed over the quench. Furthermore, we investigate the relation of the DTOP to the dynamics of the string order parameter that characterizes the topology of such systems in thermal equilibrium.
Accelerated molecular dynamics methods
Perez, Danny
2011-01-04
The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.
Punctuated equilibrium dynamics in human communications
NASA Astrophysics Data System (ADS)
Peng, Dan; Han, Xiao-Pu; Wei, Zong-Wen; Wang, Bing-Hong
2015-10-01
A minimal model based on network incorporating individual interactions is proposed to study the non-Poisson statistical properties of human behavior: individuals in system interact with their neighbors, the probability of an individual acting correlates to its activity, and all the individuals involved in action will change their activities randomly. The model reproduces varieties of spatial-temporal patterns observed in empirical studies of human daily communications, providing insight into various human activities and embracing a range of realistic social interacting systems, particularly, intriguing bimodal phenomenon. This model bridges priority queueing theory and punctuated equilibrium dynamics, and our modeling and analysis is likely to shed light on non-Poisson phenomena in many complex systems.
Static and dynamic properties of large polymer melts in equilibrium
NASA Astrophysics Data System (ADS)
Hsu, Hsiao-Ping; Kremer, Kurt
2016-04-01
We present a detailed study of the static and dynamic behaviors of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [G. Zhang et al., ACS Macro Lett. 3, 198 (2014)], we investigate their static and dynamic scaling behaviors as predicted by theory. We find that for semiflexible chains in a melt, results of the mean square internal distance, the probability distributions of the end-to-end distance, and the chain structure factor are well described by theoretical predictions for ideal chains. We examine the motion of monomers and chains by molecular dynamics simulations using the ESPResSo++ package. The scaling predictions of the mean squared displacement of inner monomers, center of mass, and relations between them based on the Rouse and the reptation theory are verified, and related characteristic relaxation times are determined. Finally, we give evidence that the entanglement length Ne,PPA as determined by a primitive path analysis (PPA) predicts a plateau modulus, GN 0 = /4 5 ( ρ k B T / N e ) , consistent with stresses obtained from the Green-Kubo relation. These comprehensively characterized equilibrium structures, which offer a good compromise between flexibility, small Ne, computational efficiency, and small deviations from ideality, provide ideal starting states for future non-equilibrium studies.
Internal Dynamics of Equilibrium Colloidal Clusters
NASA Astrophysics Data System (ADS)
Perry, Rebecca Wood
Colloidal clusters, aggregates of a few micrometer-sized spherical particles, are a model experimental system for understanding the physics of self-assembly and processes such as nucleation. Colloidal clusters are well suited for studies on these topics because they are the simplest colloidal system with internal degrees of freedom. Clusters made from particles that weakly attract one another continually rearrange between different structures. By characterizing these internal dynamics and the structures connected by the rearrangement pathways, we seek to understand the statistical physics underlying self-assembly and equilibration. In this thesis, we examine the rearrangement dynamics of colloidal clusters and analyze the equilibrium distributions of ground and excited states. We prepare clusters of up to ten microspheres bound by short-range depletion interactions that are tuned to allow equilibration between multiple isostatic arrangements. To study these clusters, we use bright-field and digital holographic microscopy paired with computational post-processing to amass ensemble-averaged and time-averaged probabilities. We study both two-dimensional (2D) and three-dimensional (3D) clusters composed of either one or two species of particles. To learn about geometrical nucleation barriers, we track rearrangements of particles within freely rotating and translating 3D clusters. We show that rearrangements occur on a timescale of seconds, consistent with diffusion-dominated internal dynamics. To better understand excited states and transition pathways, we track hundreds of rearrangements between degenerate ground states in 2D clusters. We show that the rearrangement rates can be understood using a model with two parameters, which account for the diffusion coefficient along the excited-state rearrangement pathways and the interaction potential. To explore new methods to control self-assembly, we analyze clusters of two species with different masses and different
Path integral Liouville dynamics for thermal equilibrium systems
NASA Astrophysics Data System (ADS)
Liu, Jian
2014-06-01
We show a new imaginary time path integral based method—path integral Liouville dynamics (PILD), which can be derived from the equilibrium Liouville dynamics [J. Liu and W. H. Miller, J. Chem. Phys. 134, 104101 (2011)] in the Wigner phase space. Numerical tests of PILD with the simple (white noise) Langevin thermostat have been made for two strongly anharmonic model problems. Since implementation of PILD does not request any specific form of the potential energy surface, the results suggest that PILD offers a potentially useful approach for general condensed phase molecular systems to have the two important properties: conserves the quantum canonical distribution and recovers exact thermal correlation functions (of even nonlinear operators, i.e., nonlinear functions of position or momentum operators) in the classical, high temperature, and harmonic limits.
Path integral Liouville dynamics for thermal equilibrium systems
Liu, Jian
2014-06-14
We show a new imaginary time path integral based method—path integral Liouville dynamics (PILD), which can be derived from the equilibrium Liouville dynamics [J. Liu and W. H. Miller, J. Chem. Phys. 134, 104101 (2011)] in the Wigner phase space. Numerical tests of PILD with the simple (white noise) Langevin thermostat have been made for two strongly anharmonic model problems. Since implementation of PILD does not request any specific form of the potential energy surface, the results suggest that PILD offers a potentially useful approach for general condensed phase molecular systems to have the two important properties: conserves the quantum canonical distribution and recovers exact thermal correlation functions (of even nonlinear operators, i.e., nonlinear functions of position or momentum operators) in the classical, high temperature, and harmonic limits.
Non-equilibrium hot carrier dynamics in plasmonic nanostructures
NASA Astrophysics Data System (ADS)
Narang, Prineha; Sundararaman, Ravishankar; Jermyn, Adam; Cortes, Emiliano; Maier, Stefan A.; Goddard, William A., III
Decay of surface plasmons to hot carriers is a new direction that has attracted considerable fundamental and application interest, yet a fundamental understanding of ultrafast plasmon decay processes and the underlying microscopic mechanisms remain incomplete. Ultrafast experiments provide insights into the relaxation of non-equilibrium carriers at the tens and hundreds of femtoseconds time scales, but do not yet directly probe shorter times with nanometer spatial resolution. Here we report the first ab initio calculations of non equilibrium transport of plasmonic hot carriers in metals and experimental observation of the injection of these carriers into molecules tethered to the metal surface. Specifically, metallic nanoantennas functionalized with a molecular monolayer allow for the direct probing of electron injection via surface enhanced Raman spectroscopy of the original and reduced molecular species. We combine first principles calculations of electron-electron and electron-phonon scattering rates with Boltzmann transport simulations to predict the ultrafast dynamics and transport of carriers in real materials. We also predict and compare the evolution of electron distributions in ultrafast experiments on noble metal nanoparticles.
A concurrent multiscale micromorphic molecular dynamics
Li, Shaofan Tong, Qi
2015-04-21
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.
Nonequilibrium molecular dynamics
Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )
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.
Matching pre-equilibrium dynamics and viscous hydrodynamics
Martinez, Mauricio; Strickland, Michael
2010-02-15
We demonstrate how to match pre-equilibrium dynamics of a 0+1-dimensional quark-gluon plasma to second-order viscous hydrodynamical evolution. The matching allows us to specify the initial values of the energy density and shear tensor at the initial time of hydrodynamical evolution as a function of the lifetime of the pre-equilibrium period. We compare two models for pre-equilibrium quark-gluon plasma, longitudinal free streaming and collisionally broadened longitudinal expansion, and present analytic formulas that can be used to fix the necessary components of the energy-momentum tensor. The resulting dynamical models can be used to assess the effect of pre-equilibrium dynamics on quark-gluon plasma observables. Additionally, we investigate the dependence of entropy production on pre-equilibrium dynamics and discuss the limitations of the standard definitions of nonequilibrium entropy.
Equilibrium time correlation functions and the dynamics of fluctuations
Luban, Marshall; Luscombe, James H.
1999-12-01
Equilibrium time correlation functions are of great importance because they probe the equilibrium dynamical response to external perturbations. We discuss the properties of time correlation functions for several systems that are simple enough to illustrate the calculational steps involved. The discussion underscores the need for avoiding language which misleadingly suggests that thermal equilibrium is associated with a quiescent or moribund state of the system. (c) 1999 American Association of Physics Teachers.
Equilibrium-like phase transition of a dynamic system
NASA Astrophysics Data System (ADS)
Han, Ming; Yan, Jing; Granick, Steve; Luijten, Erik
2014-03-01
Dynamic systems are considered to be intrinsically different from systems in thermal equilibrium. Despite this fundamental dichotomy, here we demonstrate that a non-equilibrium, fully dynamical system can display behavior that constitutes a complete analogy to thermal equilibrium phase behavior. This dynamical system, consisting of Janus colloids strongly controlled by external fields and over-damped by a viscous solvent, phase separates like a binary fluid mixture, with a coexistence curve separating mixed and demixed regimes and a critical point that we demonstrate to belong to the 2D Ising universality class. Within the coexistence curve, we locate the spinodal curve that separates spinodal decomposition from nucleation and growth.
Radiation in molecular dynamic simulations
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M
2008-10-13
Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.
NASA Astrophysics Data System (ADS)
Jiang, Shixiao W.; Lu, Haihao; Zhou, Douglas; Cai, David
2016-08-01
Characterizing dispersive wave turbulence in the long time dynamics is central to understanding of many natural phenomena, e.g., in atmosphere ocean dynamics, nonlinear optics, and plasma physics. Using the β-Fermi–Pasta–Ulam nonlinear system as a prototypical example, we show that in thermal equilibrium and non-equilibrium steady state the turbulent state even in the strongly nonlinear regime possesses an effective linear stochastic structure in renormalized normal variables. In this framework, we can well characterize the spatiotemporal dynamics, which are dominated by long-wavelength renormalized waves. We further demonstrate that the energy flux is nearly saturated by the long-wavelength renormalized waves in non-equilibrium steady state. The scenario of such effective linear stochastic dynamics can be extended to study turbulent states in other nonlinear wave systems.
Dynamic fracture toughness determined using molecular dynamics
Swadener, J. G.; Baskes, M. I.; Nastasi, Michael Anthony,
2004-01-01
Molecular dynamics (MD) simulations of fracture in crystalline silicon are conducted in order to determine the dynamic fracture toughness. The MD simulations show how the potential energy released during fracture is partitioned into surface energy, energy stored in defects and kinetic energy. First, the MD fracture simulations are shown to produce brittle fracture and be in reasonable agreement with experimental results. Then dynamic hcture toughness is calculated as the sum of the surface energy and the energy stored as defects directly from the MD models. Models oriented to produce fracture on either (111) or (101) planes are used. For the (101) fracture orientation, equilibrium crack speeds of greater than 80% of the Rayleigh wave speed are obtained. Crack speeds initially show a steep increase with increasing energy release rate followed by a much more gradual increase. No plateau in crack speed is observed for static energy release rates up to 20 J/m{sup 2}. At the point where the change in crack speed behavior occur, the dynamic fracture toughness (J{sub d}) is still within 10% of two times the surface energy (2{gamma}{sub 0}) and changing very slowly. From these MD simulations, it appears that the change in crack speed behavior is due to a change in the kinetic energy generation during dynamic fracture. In addition, MD simulations of facture in silicon with defects were conducted. The addition of defects increases the inelastic dissipation and the energy stored in defects.
Molecular dynamics for dense matter
NASA Astrophysics Data System (ADS)
Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi
2012-08-01
We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to 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 about 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 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 the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.
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.
Non-equilibrium dynamics of stochastic gene regulation.
Ghosh, Anandamohan
2015-01-01
The process of gene regulation is comprised of intrinsically random events resulting in large cell-to-cell variability in mRNA and protein numbers. With gene expression being the central dogma of molecular biology, it is essential to understand the origin and role of these fluctuations. An intriguing observation is that the number of mRNA present in a cell are not only random and small but also that they are produced in bursts. The gene switches between an active and an inactive state, and the active gene transcribes mRNA in bursts. Transcriptional noise being bursty, so are the number of proteins and the subsequent gene expression levels. It is natural to ask the question: what is the reason for the bursty mRNA dynamics? And can the bursty dynamics be shown to be entropically favorable by studying the reaction kinetics underlying the gene regulation mechanism? The dynamics being an out-of-equilibrium process, the fluctuation theorem for entropy production in the reversible reaction channel is discussed. We compute the entropy production rate for varying degrees of burstiness. We find that the reaction parameters that maximize the burstiness simultaneously maximize the entropy production rate. PMID:25288134
Superposition State Molecular Dynamics.
Venkatnathan, Arun; Voth, Gregory A
2005-01-01
The ergodic sampling of rough energy landscapes is crucial for understanding phenomena like protein folding, peptide aggregation, polymer dynamics, and the glass transition. These rough energy landscapes are characterized by the presence of many local minima separated by high energy barriers, where Molecular Dynamics (MD) fails to satisfy ergodicity. To enhance ergodic behavior, we have developed the Superposition State Molecular Dynamics (SSMD) method, which uses a superposition of energy states to obtain an effective potential for the MD simulation. In turn, the dynamics on this effective potential can be used to sample the configurational free energy of the real potential. The effectiveness of the SSMD method for a one-dimensional rough potential energy landscape is presented as a test case. PMID:26641113
Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands.
Valente, Luis M; Phillimore, Albert B; Etienne, Rampal S
2015-08-01
Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms. PMID:26105791
Non-equilibrium many body dynamics
Creutz, M.; Gyulassy, M.
1997-09-22
This Riken BNL Research Center Symposium on Non-Equilibrium Many Body Physics was held on September 23-25, 1997 as part of the official opening ceremony of the Center at Brookhaven National Lab. A major objective of theoretical work at the center is to elaborate on the full spectrum of strong interaction physics based on QCD, including the physics of confinement and chiral symmetry breaking, the parton structure of hadrons and nuclei, and the phenomenology of ultra-relativistic nuclear collisions related to the up-coming experiments at RHIC. The opportunities and challenges of nuclear and particle physics in this area naturally involve aspects of the many body problem common to many other fields. The aim of this symposium was to find common theoretical threads in the area of non-equilibrium physics and modern transport theories. The program consisted of invited talks on a variety topics from the fields of atomic, condensed matter, plasma, astrophysics, cosmology, and chemistry, in addition to nuclear and particle physics. Separate abstracts have been indexed into the database for contributions to this workshop.
Thermo-chemical dynamics and chemical quasi-equilibrium of plasmas in thermal non-equilibrium
Massot, Marc; Graille, Benjamin; Magin, Thierry E.
2011-05-20
We examine both processes of ionization by electron and heavy-particle impact in spatially uniform plasmas at rest in the absence of external forces. A singular perturbation analysis is used to study the following physical scenario, in which thermal relaxation becomes much slower than chemical reactions. First, electron-impact ionization is investigated. The dynamics of the system rapidly becomes close to a slow dynamics manifold that allows for defining a unique chemical quasi-equilibrium for two-temperature plasmas and proving that the second law of thermodynamics is satisfied. Then, all ionization reactions are taken into account simultaneously, leading to a surprising conclusion: the inner layer for short time scale (or time boundary layer) directly leads to thermal equilibrium. Global thermo-chemical equilibrium is reached within a short time scale, involving only chemical reactions, even if thermal relaxation through elastic collisions is assumed to be slow.
Strongly Non-equilibrium Dynamics of Nanochannel Confined DNA
NASA Astrophysics Data System (ADS)
Reisner, Walter
Nanoconfined DNA exhibits a wide-range of fascinating transient and steady-state non-equilibrium phenomena. Yet, while experiment, simulation and scaling analytics are converging on a comprehensive picture regarding the equilibrium behavior of nanochannel confined DNA, non-equilibrium behavior remains largely unexplored. In particular, while the DNA extension along the nanochannel is the key observable in equilibrium experiments, in the non-equilibrium case it is necessary to measure and model not just the extension but the molecule's full time-dependent one-dimensional concentration profile. Here, we apply controlled compressive forces to a nanochannel confined molecule via a nanodozer assay, whereby an optically trapped bead is slid down the channel at a constant speed. Upon contact with the molecule, a propagating concentration ``shockwave'' develops near the bead and the molecule is dynamically compressed. This experiment, a single-molecule implementation of a macroscopic cylinder-piston apparatus, can be used to observe the molecule response over a range of forcings and benchmark theoretical description of non-equilibrium behavior. We show that the dynamic concentration profiles, including both transient and steady-state response, can be modelled via a partial differential evolution equation combining nonlinear diffusion and convection. Lastly, we present preliminary results for dynamic compression of multiple confined molecules to explore regimes of segregation and mixing for multiple chains in confinement.
Evolution of specialization under non-equilibrium population dynamics.
Nurmi, Tuomas; Parvinen, Kalle
2013-03-21
We analyze the evolution of specialization in resource utilization in a mechanistically underpinned discrete-time model using the adaptive dynamics approach. We assume two nutritionally equivalent resources that in the absence of consumers grow sigmoidally towards a resource-specific carrying capacity. The consumers use resources according to the law of mass-action with rates involving trade-off. The resulting discrete-time model for the consumer population has over-compensatory dynamics. We illuminate the way non-equilibrium population dynamics affect the evolutionary dynamics of the resource consumption rates, and show that evolution to the trimorphic coexistence of a generalist and two specialists is possible due to asynchronous non-equilibrium population dynamics of the specialists. In addition, various forms of cyclic evolutionary dynamics are possible. Furthermore, evolutionary suicide may occur even without Allee effects and demographic stochasticity. PMID:23306058
Step-wise pulling protocols for non-equilibrium dynamics
NASA Astrophysics Data System (ADS)
Ngo, Van Anh
ensembles, which can be used to characterize non-equilibrium dynamics. Furthermore, we have applied the stepwise pulling protocols and Jarzynski's Equality to investigate the ion selectivity of potassium channels via molecular dynamics simulations. The mechanism of the potassium ion selectivity has remained poorly understood for over fifty years, although a Nobel Prize was awarded to the discovery of the molecular structure of a potassium-selective channel in 2003. In one year of performing simulations, we were able to reproduce the major results of ion selectivity accumulated in fifty years. We have been even boldly going further to propose a new model for ion selectivity based on the structural rearrangement of the selectivity filter of potassium-selective KcsA channels. This structural rearrangement has never been shown to play such a pivotal role in selecting and conducting potassium ions, but effectively rejecting sodium ions. Using the stepwise pulling protocols, we are also able to estimate conductance for ion channels, which remains elusive by using other methods. In the light of ion channels, we have also investigated how a synthetic channel of telemeric G-quadruplex conducts different types of ions. These two studies on ion selectivity not only constitute an interesting part of this dissertation, but also will enable us to further explore a new set of ion-selectivity principles. Beside the focus of my dissertation, I used million-atom molecular dynamics simulations to investigate the mechanical properties of body-centered-cubic (BCCS) and face-centered-cubic (FCCS) supercrystals of DNA-functionalized gold nanoparticles. These properties are valuable for examining whether these supercrystals can be used in gene delivery and gene therapy. The formation of such ordered supercrystals is useful to protect DNAs or RNAs from being attacked and destroyed by enzymes in cells. I also performed all-atom molecular dynamics simulations to study a pure oleic acid (OA) membrane
Non Equilibrium Transformations of Molecular Compounds Induced Mechanically
Descamps, M.; Willart, J. F.; Dudognon, E.
2006-05-05
Results clarifying the effects of mechanical milling on molecular solids are shortly reviewed. Special attention has been paid to the temperature of milling with regard to the glass transition temperature of the compounds. It is shown that decreasing the grinding temperature has for incidence to increase the amorphization tendency whereas milling above Tg produces a crystal-to-crystal transformation between polymorphic varieties. These observations contradict the usual proposition that grinding transforms the physical state only by a heating effect which induces a local melting. Equilibrium thermodynamics does not seem to be appropriate for describing the process. The driven alloys concept offers a more rational framework to interpret the effect of the milling temperature. Other results are presented which demonstrate the possibility for grinding to realize low temperature solid state alloying which offers new promising ways to stabilize amorphous molecular solids. In a second part the effect of dehydration of a molecular hydrate is described. It is shown that the rate of the dehydration process is a driving force for this other type of mechanical non equilibrium transformation.
Molecular Dynamics of Acetylcholinesterase
Shen, T Y.; Tai, Kaihsu; Henchman, Richard H.; Mccammon, Andy
2002-06-01
Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.
Non-Equilibrium Water-Glassy Polymer Dynamics
NASA Astrophysics Data System (ADS)
Davis, Eric; Minelli, Matteo; Baschetti, Marco; Sarti, Giulio; Elabd, Yossef
2012-02-01
For many applications (e.g., medical implants, packaging), an accurate assessment and fundamental understanding of the dynamics of water-glassy polymer interactions is of great interest. In this study, sorption and diffusion of pure water in several glassy polymers films, such as poly(styrene) (PS), poly(methyl methacrylate) (PMMA), poly(lactide) (PLA), were measured over a wide range of vapor activities and temperatures using several experimental techniques, including quartz spring microbalance (QSM), quartz crystal microbalance (QCM), and time-resolved Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy. Non-Fickian behavior (diffusion-relaxation phenomena) was observed by all three techniques, while FTIR-ATR spectroscopy also provides information about the distribution of the states of water and water transport mechanisms on a molecular-level. Specifically, the states of water are significantly different in PS compared to PMMA and PLA. Additionally, a purely predictive non-equilibrium lattice fluid (NELF) model was applied to predict the sorption isotherms of water in these glassy polymers.
Towards Non-Equilibrium Dynamics with Trapped Ions
NASA Astrophysics Data System (ADS)
Silbert, Ariel; Jubin, Sierra; Doret, Charlie
2016-05-01
Atomic systems are superbly suited to the study of non-equilibrium dynamics. These systems' exquisite isolation from environmental perturbations leads to long relaxation times that enable exploration of far-from-equilibrium phenomena. One example of particular relevance to experiments in trapped ion quantum information processing, metrology, and precision spectroscopy is the approach to thermal equilibrium of sympathetically cooled linear ion chains. Suitable manipulation of experimental parameters permits exploration of the quantum-to-classical crossover between ballistic transport and diffusive, Fourier's Law conduction, a topic of interest not only to the trapped ion community but also for the development of microelectronic devices and other nanoscale structures. We present progress towards trapping chains of multiple co-trapped calcium isotopes geared towards measuring thermal equilibration and discuss plans for future experiments in non-equilibrium statistical mechanics. This work is supported by Cottrell College Science Award from the Research Corporation for Science Advancement and by Williams College.
Wong, Albert S Y; Postma, Sjoerd G J; Vialshin, Ilia N; Semenov, Sergey N; Huck, Wilhelm T S
2015-09-30
Our knowledge of the properties and dynamics of complex molecular reaction networks, for example those found in living systems, considerably lags behind the understanding of elementary chemical reactions. In part, this is because chemical reactions networks are nonlinear systems that operate under conditions far from equilibrium. Of particular interest is the role of individual reaction rates on the stability of the network output. In this research we use a rational approach combined with computational methods, to produce complex behavior (in our case oscillations) and show that small changes in molecular structure are sufficient to impart large changes in network behavior. PMID:26352485
Multiscale reactive molecular dynamics
NASA Astrophysics Data System (ADS)
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-12-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
Equilibrium and Disequilibrium Dynamics in Cobweb Models with Time Delays
NASA Astrophysics Data System (ADS)
Gori, Luca; Guerrini, Luca; Sodini, Mauro
2015-06-01
This paper aims to study price dynamics in two different continuous time cobweb models with delays close to [Hommes, 1994]. In both cases, the stationary equilibrium may be not representative of the long-term dynamics of the model, since it is possible to observe endogenous and persistent fluctuations (supercritical Hopf bifurcations) even if a deterministic context without external shocks is considered. In the model in which markets are in equilibrium every time, we show that the existence of time delays in the expectations formation mechanism may cause chaotic dynamics similar to those obtained in [Hommes, 1994] in a discrete time context. From a mathematical point of view, we apply the Poincaré-Lindstedt perturbation method to study the local dynamic properties of the models. In addition, several numerical experiments are used to investigate global properties of the systems.
Replica-symmetry-breaking transitions and off-equilibrium dynamics
NASA Astrophysics Data System (ADS)
Rizzo, Tommaso
2013-09-01
I consider branches of replica-symmetry-breaking (RSB) solutions in glassy systems that display a dynamical transition at a temperature Td characterized by a mode-coupling-theory dynamical behavior. Below Td these branches of solutions are considered to be relevant to the system complexity and to off-equilibrium dynamics. Under general assumptions I argue that near Td it is not possible to stabilize the one-step (1RSB) solution beyond the marginal point by making a full RSB (FRSB) ansatz. However, depending on the model, there may exist a temperature T* strictly lower than Td below which the 1RSB branch can be continued to a FRSB branch. Such a temperature certainly exists for models that display the so-called Gardner transition and in this case TG
Punctuated equilibrium and power law in economic dynamics
NASA Astrophysics Data System (ADS)
Gupta, Abhijit Kar
2012-02-01
This work is primarily based on a recently proposed toy model by Thurner et al. (2010) [3] on Schumpeterian economic dynamics (inspired by the idea of economist Joseph Schumpeter [9]). Interestingly, punctuated equilibrium has been shown to emerge from the dynamics. The punctuated equilibrium and Power law are known to be associated with similar kinds of biologically relevant evolutionary models proposed in the past. The occurrence of the Power law is a signature of Self-Organised Criticality (SOC). In our view, power laws can be obtained by controlling the dynamics through incorporating the idea of feedback into the algorithm in some way. The so-called 'feedback' was achieved by introducing the idea of fitness and selection processes in the biological evolutionary models. Therefore, we examine the possible emergence of a power law by invoking the concepts of 'fitness' and 'selection' in the present model of economic evolution.
Chemical equilibrium in high pressure molecular fluid mixtures
Shaw, M.S.
1993-09-01
The N{sub atoms}PT Monte Carlo simulation method has been reformulated to incorporate multiple species and chemical reactions with changes in total number of molecules. While maintaining a constant number of each type of atom, the number of molecules is changed by turning on and off the interactions of any particular position with other molecules. Chemical reactions are allowed as a correlated move of atoms to differnt molecular locations. Equilibrium chemical composition is determined as an average over the simulation along with equation of state quantities. A large set of simulations has been made with the system N{sub 2} + O{sub 2} {rightleftharpoons} NO covering a wide range in P and T. Both Hugoniot states and the CJ point have been determined and are shown to be sensitive to the potentials between unlike species.
Glass formers display universal non-equilibrium dynamics on the level of single-particle jumps
NASA Astrophysics Data System (ADS)
Helfferich, J.; Vollmayr-Lee, K.; Ziebert, F.; Meyer, H.; Baschnagel, J.
2015-02-01
Glasses are inherently out-of-equilibrium systems evolving slowly toward their equilibrium state in a process called physical aging. During aging, dynamic observables depend on the history of the system, hampering comparative studies of dynamics in different glass formers. Here, we demonstrate how glass formers can be directly compared on the level of single-particle jumps, i.e. the structural relaxation events underlying the α-process. Describing the dynamics in terms of a continuous-time random walk, an analytic prediction for the jump rate is derived. The result is subsequently compared to molecular-dynamics simulations of amorphous silica and a polymer melt as two generic representatives of strong and fragile glass formers, and good agreement is found.
Chen, Yunjie; Roux, Benoît
2015-01-14
A family of hybrid simulation methods that combines the advantages of Monte Carlo (MC) with the strengths of classical molecular dynamics (MD) consists in carrying out short non-equilibrium MD (neMD) trajectories to generate new configurations that are subsequently accepted or rejected via an MC process. In the simplest case where a deterministic dynamic propagator is used to generate the neMD trajectories, the familiar Metropolis acceptance criterion based on the change in the total energy ΔE, min[1, exp( − βΔE)], guarantees that the hybrid algorithm will yield the equilibrium Boltzmann distribution. However, the functional form of the acceptance probability is more complex when the non-equilibrium switching process is generated via a non-deterministic stochastic dissipative propagator coupled to a heat bath. Here, we clarify the conditions under which the Metropolis criterion remains valid to rigorously yield a proper equilibrium Boltzmann distribution within hybrid neMD-MC algorithm.
Introduction to Accelerated Molecular Dynamics
Perez, Danny
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
Molecular Dynamics Calculations
NASA Technical Reports Server (NTRS)
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
Molecular dynamics simulations
Alder, B.J.
1985-07-01
The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs.
VMD: visual molecular dynamics.
Humphrey, W; Dalke, A; Schulten, K
1996-02-01
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web. PMID:8744570
Non-equilibrium dynamics in AMO quantum simulators
NASA Astrophysics Data System (ADS)
Daley, Andrew
2016-05-01
Recently, the possibility to control and measure AMO systems time-dependently has generated a lot of progress in exploring out-of-equilibrium dynamics for strongly interacting many-particle systems. This connects directly to fundamental questions relating to the relaxation of such systems to equilibrium, as well as the spreading of correlations and build-up of entanglement. While ultracold atoms allow for exceptional microscopic control over quantum gases with short-range interactions, experiments with polar molecules and chains of trapped ions now also offer the possibility to investigate spin models with long-range interactions. I will give an introduction to the recent developments in this area, illustrated with two examples: (i) the possibility to measurement entanglement for many itinerant particles with ultracold atoms in optical lattices, and (ii) new opportunities to compare dynamics with short and long-range interactions, especially using systems of trapped ions, where it is possible to control the effective range of interactions.
Biological Implications of Dynamical Phases in Non-equilibrium Networks
NASA Astrophysics Data System (ADS)
Murugan, Arvind; Vaikuntanathan, Suriyanarayanan
2016-03-01
Biology achieves novel functions like error correction, ultra-sensitivity and accurate concentration measurement at the expense of free energy through Maxwell Demon-like mechanisms. The design principles and free energy trade-offs have been studied for a variety of such mechanisms. In this review, we emphasize a perspective based on dynamical phases that can explain commonalities shared by these mechanisms. Dynamical phases are defined by typical trajectories executed by non-equilibrium systems in the space of internal states. We find that coexistence of dynamical phases can have dramatic consequences for function vs free energy cost trade-offs. Dynamical phases can also provide an intuitive picture of the design principles behind such biological Maxwell Demons.
Floating orbital molecular dynamics simulations.
Perlt, Eva; Brüssel, Marc; Kirchner, Barbara
2014-04-21
We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated. PMID:24600690
Molecular dynamics simulations of supramolecular polymer rheology
NASA Astrophysics Data System (ADS)
Li, Zhenlong; Djohari, Hadrian; Dormidontova, Elena E.
2010-11-01
Using equilibrium and nonequilibrium molecular dynamics simulations, we studied the equilibrium and rheological properties of dilute and semidilute solutions of head-to-tail associating polymers. In our simulation model, a spontaneous complementary reversible association between the donor and the acceptor groups at the ends of oligomers was achieved by introducing a combination of truncated pseudo-Coulombic attractive potential and Lennard Jones repulsive potential between donor, acceptor, and neighboring groups. We have calculated the equilibrium properties of supramolecular polymers, such as the ring/chain equilibrium, average molecular weight, and molecular weight distribution of self-assembled chains and rings, which all agree well with previous analytical and computer modeling results. We have investigated shear thinning of solutions of 8- and 20-bead associating oligomers with different association energies at different temperatures and oligomer volume fractions. All reduced viscosity data for a given oligomer length can be collapsed into one master curve, exhibiting two power-law regions of shear-thinning behavior with an exponent of -0.55 at intermediate ranges of the reduced shear rate β and -0.8 (or -0.9) at larger shear rates. The equilibrium viscosity of supramolecular solutions with different oligomer lengths and associating energies is found to obey a power-law scaling dependence on oligomer volume fraction with an exponent of 1.5, in agreement with the experimental observations for several dilute or semidilute solutions of supramolecular polymers. This implies that dilute and semidilute supramolecular polymer solutions exhibit high polydispersity but may not be sufficiently entangled to follow the reptation mechanism of relaxation.
Vegetation ecogeomorphology, dynamic equilibrium, and disturbance: chapter 7
Hupp, Cliff R.
2013-01-01
Early ecologists understood the need to document geomorphic form and process to explain plant species distributions. Although this relationship has been acknowledged for over a century, with the exception of a few landmark papers, only the past few decades have experienced intensive research on this interdisciplinary topic. Here the authors provide a summary of the intimate relations between vegetation and geomorphic/process on hillslopes and fluvial systems. These relations are separated into systems (primarily fluvial) in dynamic equilibrium and those that are in nonequilibrium conditions including the impacts of various human disturbances affecting landforms, geomorphic processes, and interrelated, attendant vegetation patterns and processes. The authors conclude with a conceptual model of stream regime focusing on sediment deposition, erosion, and equilibrium that can be expanded to organize and predict vegetation patterns and life history strategies.
Nash equilibrium and evolutionary dynamics in semifinalists' dilemma
NASA Astrophysics Data System (ADS)
Baek, Seung Ki; Son, Seung-Woo; Jeong, Hyeong-Chai
2015-04-01
We consider a tournament among four equally strong semifinalists. The players have to decide how much stamina to use in the semifinals, provided that the rest is available in the final and the third-place playoff. We investigate optimal strategies for allocating stamina to the successive matches when players' prizes (payoffs) are given according to the tournament results. From the basic assumption that the probability to win a match follows a nondecreasing function of stamina difference, we present symmetric Nash equilibria for general payoff structures. We find three different phases of the Nash equilibria in the payoff space. First, when the champion wins a much bigger payoff than the others, any pure strategy can constitute a Nash equilibrium as long as all four players adopt it in common. Second, when the first two places are much more valuable than the other two, the only Nash equilibrium is such that everyone uses a pure strategy investing all stamina in the semifinal. Third, when the payoff for last place is much smaller than the others, a Nash equilibrium is formed when every player adopts a mixed strategy of using all or none of its stamina in the semifinals. In a limiting case that only last place pays the penalty, this mixed-strategy profile can be proved to be a unique symmetric Nash equilibrium, at least when the winning probability follows a Heaviside step function. Moreover, by using this Heaviside step function, we study the tournament by using evolutionary replicator dynamics to obtain analytic solutions, which reproduces the corresponding Nash equilibria on the population level and gives information on dynamic aspects.
Nash equilibrium and evolutionary dynamics in semifinalists' dilemma.
Baek, Seung Ki; Son, Seung-Woo; Jeong, Hyeong-Chai
2015-04-01
We consider a tournament among four equally strong semifinalists. The players have to decide how much stamina to use in the semifinals, provided that the rest is available in the final and the third-place playoff. We investigate optimal strategies for allocating stamina to the successive matches when players' prizes (payoffs) are given according to the tournament results. From the basic assumption that the probability to win a match follows a nondecreasing function of stamina difference, we present symmetric Nash equilibria for general payoff structures. We find three different phases of the Nash equilibria in the payoff space. First, when the champion wins a much bigger payoff than the others, any pure strategy can constitute a Nash equilibrium as long as all four players adopt it in common. Second, when the first two places are much more valuable than the other two, the only Nash equilibrium is such that everyone uses a pure strategy investing all stamina in the semifinal. Third, when the payoff for last place is much smaller than the others, a Nash equilibrium is formed when every player adopts a mixed strategy of using all or none of its stamina in the semifinals. In a limiting case that only last place pays the penalty, this mixed-strategy profile can be proved to be a unique symmetric Nash equilibrium, at least when the winning probability follows a Heaviside step function. Moreover, by using this Heaviside step function, we study the tournament by using evolutionary replicator dynamics to obtain analytic solutions, which reproduces the corresponding Nash equilibria on the population level and gives information on dynamic aspects. PMID:25974475
Dynamic equilibrium explanation for nanobubbles' unusual temperature and saturation dependence
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Shell, M. Scott; Leal, L. Gary
2013-07-01
The dynamic equilibrium model suggests that surface nanobubbles can be stable due to an influx of gas in the vicinity of the bubble contact line, driven by substrate hydrophobicity, that balances the outflux of gas from the bubble apex. Here, we develop an alternate formulation of this mechanism that predicts rich behavior in agreement with recent experimental measurements. Namely, we find that stable nanobubbles exist in narrow temperature and dissolved gas concentration ranges, that there is a maximum and minimum possible bubble size, and that nanobubble radii decrease with temperature.
Equilibrium thermodynamics of multiply substituted isotopologues of molecular gases
NASA Astrophysics Data System (ADS)
Wang, Zhengrong; Schauble, Edwin A.; Eiler, John M.
2004-12-01
Isotopologues of molecular gases containing more than one rare isotope (multiply substituted isotopologues) can be analyzed with high precision (1σ <0.1 ‰), despite their low natural abundances (˜ ppm to ppt in air), and can constrain geochemical budgets of natural systems. We derive a method for calculating abundances of all such species in a thermodynamically equilibrated population of isotopologues, and present results of these calculations for O 2, CO, N 2, NO, CO 2, and N 2O between 1000 and 193 to 77 K. In most cases, multiply substituted isotopologues are predicted to be enriched relative to stochastic (random) distributions by ca. 1 to 2 ‰ at earth-surface temperatures. This deviation, defined as Δ i for isotopologue i, generally increases linearly with 1/T at temperatures ≤ 500 K. An exception is N 2O, which shows complex temperature dependences and 10's of per-mill enrichments or depletions of abundances for some isotopologues. These calculations provide a basis for discriminating between fractionations controlled by equilibrium thermodynamics and other sorts of isotopic fractionations in the budgets of atmospheric gases. Moreover, because abundances of multiply substituted isotopologues in thermodynamically equilibrated populations of molecules vary systematically with temperature, they can be used as geothermometers. Such thermometers are unusual in that they involve homogeneous rather than heterogeneous equilibria (e.g., isotopic distribution in gaseous CO 2 alone, rather than difference in isotopic composition between CO 2 and coexisting water). Also, multiple independent thermometers exist for all molecules having more than one multiply substituted isotopologue (e.g., thermometers based on abundances of 18O 13C 16O and 18O 12C 18O are independent); thus, temperatures estimated by this method can be tested for internal consistency.
Molecular Dynamics Simulations of Water Evaporation
NASA Astrophysics Data System (ADS)
Wen, Chengyuan; Grest, Gary; Cheng, Shengfeng
2015-03-01
The evaporation of water from the liquid/vapor interface is studied via large-scale molecular dynamics simulations for systems of more than a million atoms at 550K and 600K. The TIP4P-2005 water model whose liquid/vapor surface tension is in excellent agreement with experiments is used. Evaporative cooling at the interface is observed from temperature profiles determined from both translational and rotational kinetic energy. During evaporation, the density of water is slightly enhanced near the liquid-vapor interface. The velocity distribution of water molecules in the vapor phase during evaporation at various distances relative to the interface fit a Maxwell-Boltzmann distribution. While our results indicate an imbalance between evaporating and condensing water molecules, local thermal equilibrium is found to hold in addition to mechanical equilibrium. Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus.
Martinez, Pierre; Timmer, Margriet R; Lau, Chiu T; Calpe, Silvia; Sancho-Serra, Maria Del Carmen; Straub, Danielle; Baker, Ann-Marie; Meijer, Sybren L; Kate, Fiebo J W Ten; Mallant-Hent, Rosalie C; Naber, Anton H J; van Oijen, Arnoud H A M; Baak, Lubbertus C; Scholten, Pieter; Böhmer, Clarisse J M; Fockens, Paul; Bergman, Jacques J G H M; Maley, Carlo C; Graham, Trevor A; Krishnadath, Kausilia K
2016-01-01
Surveillance of Barrett's oesophagus allows us to study the evolutionary dynamics of a human neoplasm over time. Here we use multicolour fluorescence in situ hybridization on brush cytology specimens, from two time points with a median interval of 37 months in 195 non-dysplastic Barrett's patients, and a third time point in a subset of 90 patients at a median interval of 36 months, to study clonal evolution at single-cell resolution. Baseline genetic diversity predicts progression and remains in a stable dynamic equilibrium over time. Clonal expansions are rare, being detected once every 36.8 patient years, and growing at an average rate of 1.58 cm(2) (95% CI: 0.09-4.06) per year, often involving the p16 locus. This suggests a lack of strong clonal selection in Barrett's and that the malignant potential of 'benign' Barrett's lesions is predetermined, with important implications for surveillance programs. PMID:27538785
Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus
Martinez, Pierre; Timmer, Margriet R.; Lau, Chiu T.; Calpe, Silvia; Sancho-Serra, Maria del Carmen; Straub, Danielle; Baker, Ann-Marie; Meijer, Sybren L.; Kate, Fiebo J. W. ten; Mallant-Hent, Rosalie C.; Naber, Anton H. J.; van Oijen, Arnoud H. A. M.; Baak, Lubbertus C.; Scholten, Pieter; Böhmer, Clarisse J. M.; Fockens, Paul; Bergman, Jacques J. G. H. M.; Maley, Carlo C.; Graham, Trevor A.; Krishnadath, Kausilia K
2016-01-01
Surveillance of Barrett's oesophagus allows us to study the evolutionary dynamics of a human neoplasm over time. Here we use multicolour fluorescence in situ hybridization on brush cytology specimens, from two time points with a median interval of 37 months in 195 non-dysplastic Barrett's patients, and a third time point in a subset of 90 patients at a median interval of 36 months, to study clonal evolution at single-cell resolution. Baseline genetic diversity predicts progression and remains in a stable dynamic equilibrium over time. Clonal expansions are rare, being detected once every 36.8 patient years, and growing at an average rate of 1.58 cm2 (95% CI: 0.09–4.06) per year, often involving the p16 locus. This suggests a lack of strong clonal selection in Barrett's and that the malignant potential of ‘benign' Barrett's lesions is predetermined, with important implications for surveillance programs. PMID:27538785
Equilibrium Analysis of a Yellow Fever Dynamical Model with Vaccination
Martorano Raimundo, Silvia
2015-01-01
We propose an equilibrium analysis of a dynamical model of yellow fever transmission in the presence of a vaccine. The model considers both human and vector populations. We found thresholds parameters that affect the development of the disease and the infectious status of the human population in the presence of a vaccine whose protection may wane over time. In particular, we derived a threshold vaccination rate, above which the disease would be eradicated from the human population. We show that if the mortality rate of the mosquitoes is greater than a given threshold, then the disease is naturally (without intervention) eradicated from the population. In contrast, if the mortality rate of the mosquitoes is less than that threshold, then the disease is eradicated from the populations only when the growing rate of humans is less than another threshold; otherwise, the disease is eradicated only if the reproduction number of the infection after vaccination is less than 1. When this reproduction number is greater than 1, the disease will be eradicated from the human population if the vaccination rate is greater than a given threshold; otherwise, the disease will establish itself among humans, reaching a stable endemic equilibrium. The analysis presented in this paper can be useful, both to the better understanding of the disease dynamics and also for the planning of vaccination strategies. PMID:25834634
Molecular photoionization dynamics
Dehmer, Joseph L.
1982-05-01
This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed. (WHK)
Molecular dynamics simulation of liquid sulfur dioxide.
Ribeiro, Mauro C C
2006-05-01
A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k). PMID:16640437
Molecular finite-size effects in stochastic models of equilibrium chemical systems.
Cianci, Claudia; Smith, Stephen; Grima, Ramon
2016-02-28
The reaction-diffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are point-like. Here, we introduce the excluded volume reaction-diffusion master equation (vRDME) which takes into account volume exclusion effects on stochastic kinetics due to a finite molecular radius. We obtain an exact closed form solution of the RDME and of the vRDME for a general chemical system in equilibrium conditions. The difference between the two solutions increases with the ratio of molecular diameter to the compartment length scale. We show that an increase in the fraction of excluded space can (i) lead to deviations from the classical inverse square root law for the noise-strength, (ii) flip the skewness of the probability distribution from right to left-skewed, (iii) shift the equilibrium of bimolecular reactions so that more product molecules are formed, and (iv) strongly modulate the Fano factors and coefficients of variation. These volume exclusion effects are found to be particularly pronounced for chemical species not involved in chemical conservation laws. Finally, we show that statistics obtained using the vRDME are in good agreement with those obtained from Brownian dynamics with excluded volume interactions. PMID:26931675
Molecular finite-size effects in stochastic models of equilibrium chemical systems
NASA Astrophysics Data System (ADS)
Cianci, Claudia; Smith, Stephen; Grima, Ramon
2016-02-01
The reaction-diffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are point-like. Here, we introduce the excluded volume reaction-diffusion master equation (vRDME) which takes into account volume exclusion effects on stochastic kinetics due to a finite molecular radius. We obtain an exact closed form solution of the RDME and of the vRDME for a general chemical system in equilibrium conditions. The difference between the two solutions increases with the ratio of molecular diameter to the compartment length scale. We show that an increase in the fraction of excluded space can (i) lead to deviations from the classical inverse square root law for the noise-strength, (ii) flip the skewness of the probability distribution from right to left-skewed, (iii) shift the equilibrium of bimolecular reactions so that more product molecules are formed, and (iv) strongly modulate the Fano factors and coefficients of variation. These volume exclusion effects are found to be particularly pronounced for chemical species not involved in chemical conservation laws. Finally, we show that statistics obtained using the vRDME are in good agreement with those obtained from Brownian dynamics with excluded volume interactions.
Dynamic-domain-decomposition parallel molecular dynamics
NASA Astrophysics Data System (ADS)
Srinivasan, S. G.; Ashok, I.; Jônsson, Hannes; Kalonji, Gretchen; Zahorjan, John
1997-05-01
Parallel molecular dynamics with short-range forces can suffer from load-imbalance problems and attendant performance degradation due to density variations in the simulated system. In this paper, we describe an approach to dynamical load balancing, enabled by the Ādhāra runtime system. The domain assigned to each processor is automatically and dynamically resized so as to evenly distribute the molecular dynamics computations across all the processors. The algorithm was tested on an Intel Paragon parallel computer for two and three-dimensional Lennard-Jones systems containing 99 458 and 256000 atoms, respectively, and using up to 256 processors. In these benchmarks, the overhead for carrying out the load-balancing operations was found to be small and the total computation time was reduced by as much as 50%.
Flexible polymers and thin rods far from equilibrium: buckling dynamics
Golubovic; Moldovan; Peredera
2000-02-01
We investigate the dynamics of the classical Euler buckling instability of compressed objects such as flexible molecular chains and thin rods moving in a viscous medium. We find that flexible chains undergo a coarsening process self-similar in time. They develop a wavelike pattern whose amplitude and wavelength grow in time. We relate the buckling dynamics to phase ordering phenomena. The role of the order parameter here is played by the chain slope with respect to the straight initial chain configuration. PMID:11046455
Onset of cooperative dynamics in equilibrium glass-forming metallic liquids
NASA Astrophysics Data System (ADS)
Jaiswal, Abhishek; Zhang, Yang
Onset of cooperative dynamics has been observed in the metastable regime of many molecular liquids, colloids, and granular materials approaching their respective glass or jamming transition points. It is also considered to play a significant role in the emergence of slow dynamics. However, the nature of such dynamical cooperativity remains elusive in multicomponent metallic liquids characterized by complex many-body interactions and high mixing entropy. Herein, we report indications of the onset of cooperative dynamics in an equilibrium glass-forming metallic liquid (ZrCuNiAl). This is revealed by deviation of the experimentally measured mean diffusion coefficient from its high temperature Arrhenius behavior below To ~ 1300 K, i.e., a crossover from uncorrelated dynamics above To to landscape-influenced correlated dynamics below To. The onset/crossover in this system is observed at approximately twice of its calorimetric glass transition temperature (Tg ~ 697 K) and in the stable liquid phase, unlike many molecular liquids. Furthermore, we show the presence of such a dynamical onset phenomenon in ten other glass-forming metallic liquids, universally occurring at approximately twice of their Tg and in their liquid phases.
Non-equilibrium dynamics in driven Bose-Einstein condensates
NASA Astrophysics Data System (ADS)
Feng, Lei; Clark, Logan W.; Ha, Li-Chung; Chin, Cheng
2016-05-01
We report recent progress on the study of non-equilibrium dynamics in Bose-Einstein condensates using the shaken optical lattice or optically controlled Feshbach resonances. In the shaken lattice at sufficient shaking amplitude we observe a quantum phase transition from ordinary condensates to pseudo-spinor 1/2 condensates containing discrete domains with effective ferromagnetic interactions. We study the temporal and spatial Kibble-Zurek scaling laws for the dependence of this domain structure on the quench rate across the transition. Furthermore, we observe long-range density correlations within the ferromagnetic condensate. With optically controlled Feshbach resonances we demonstrate control of the interaction strength between atoms at timescales as short as ten nanoseconds and length scales smaller than the condensate. We find that making interactions attractive within only one region of the gas induces localized collapse of the condensate.
Dynamic equilibrium explanation for nanobubbles unusual temperature and saturation dependence
NASA Astrophysics Data System (ADS)
Leal, L. Gary
2013-11-01
Recent experimental evidence demonstrates that nanobubbles exhibit unusual behavior in response to changes in temperature and gas saturation in the liquid, an observation that may shed light on the mysterious origin of their stability. In this talk, we discuss an alternate formulation of the dynamic equilibrium mechanism for nanobubbles that predicts rich behavior in agreement with these measurements. Namely, we show that stable nanobubbles exist in narrow temperature and dissolved gas concentration ranges, that there is a maximum and minimum possible bubble size, and that nanobubble radii decrease with temperature. We also discuss these predictions in the context of other current hypotheses for nanobubble stability such as the recently-proposed diffusive ``traffic jam'' model.
Microcomputer Calculation of Equilibrium Constants from Molecular Parameters of Gases.
ERIC Educational Resources Information Center
Venugopalan, Mundiyath
1989-01-01
Lists a BASIC program which computes the equilibrium constant as a function of temperature. Suggests use by undergraduates taking a one-year calculus-based physical chemistry course. Notes the program provides for up to four species, typically two reactants and two products. (MVL)
The molecular photo-cell: quantum transport and energy conversion at strong non-equilibrium.
Ajisaka, Shigeru; Žunkovič, Bojan; Dubi, Yonatan
2015-01-01
The molecular photo-cell is a single molecular donor-acceptor complex attached to electrodes and subject to external illumination. Besides the obvious relevance to molecular photo-voltaics, the molecular photo-cell is of interest being a paradigmatic example for a system that inherently operates in out-of-equilibrium conditions and typically far from the linear response regime. Moreover, this system includes electrons, phonons and photons, and environments which induce coherent and incoherent processes, making it a challenging system to address theoretically. Here, using an open quantum systems approach, we analyze the non-equilibrium transport properties and energy conversion performance of a molecular photo-cell, including both coherent and incoherent processes and treating electrons, photons, and phonons on an equal footing. We find that both the non-equilibrium conditions and decoherence play a crucial role in determining the performance of the photovoltaic conversion and the optimal energy configuration of the molecular system. PMID:25660494
The Molecular Photo-Cell: Quantum Transport and Energy Conversion at Strong Non-Equilibrium
Ajisaka, Shigeru; Žunkovič, Bojan; Dubi, Yonatan
2015-01-01
The molecular photo-cell is a single molecular donor-acceptor complex attached to electrodes and subject to external illumination. Besides the obvious relevance to molecular photo-voltaics, the molecular photo-cell is of interest being a paradigmatic example for a system that inherently operates in out-of-equilibrium conditions and typically far from the linear response regime. Moreover, this system includes electrons, phonons and photons, and environments which induce coherent and incoherent processes, making it a challenging system to address theoretically. Here, using an open quantum systems approach, we analyze the non-equilibrium transport properties and energy conversion performance of a molecular photo-cell, including both coherent and incoherent processes and treating electrons, photons, and phonons on an equal footing. We find that both the non-equilibrium conditions and decoherence play a crucial role in determining the performance of the photovoltaic conversion and the optimal energy configuration of the molecular system. PMID:25660494
Onset of Cooperative Dynamics in an Equilibrium Glass-Forming Metallic Liquid.
Jaiswal, Abhishek; O'Keeffe, Stephanie; Mills, Rebecca; Podlesynak, Andrey; Ehlers, Georg; Dmowski, Wojciech; Lokshin, Konstantin; Stevick, Joseph; Egami, Takeshi; Zhang, Yang
2016-02-18
Onset of cooperative dynamics has been observed in many molecular liquids, colloids, and granular materials in the metastable regime on approaching their respective glass or jamming transition points, and is considered to play a significant role in the emergence of the slow dynamics. However, the nature of such dynamical cooperativity remains elusive in multicomponent metallic liquids characterized by complex many-body interactions and high mixing entropy. Herein, we report evidence of onset of cooperative dynamics in an equilibrium glass-forming metallic liquid (LM601: Zr51Cu36Ni4Al9). This is revealed by deviation of the mean effective diffusion coefficient from its high-temperature Arrhenius behavior below TA ≈ 1300 K, i.e., a crossover from uncorrelated dynamics above TA to landscape-influenced correlated dynamics below TA. Furthermore, the onset/crossover temperature TA in such a multicomponent bulk metallic glass-forming liquid is observed at approximately twice of its calorimetric glass transition temperature (Tg ≈ 697 K) and in its stable liquid phase, unlike many molecular liquids. PMID:26798946
Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Byutner, Oleksiy; Smith, Grant
2001-03-01
In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.
Molecular dynamics and protein function
Karplus, M.; Kuriyan, J.
2005-01-01
A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. 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 with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F1 ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems. PMID:15870208
A sampling of molecular dynamics
NASA Astrophysics Data System (ADS)
Sindhikara, Daniel Jon
The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: increasing efficiency, measuring convergence, avoiding pitfalls, and an application and analysis of a biological system. Chapters 3 and 4 deal with an enhanced sampling algorithm called "replica exchange molecular dynamics" which is designed to speed-up molecular dynamics simulations. The optimization of a key parameter of these simulations is analyzed. In these successive projects, it was found conclusively that maximizing "exchange attempt frequency" is the most efficient way to run a replica exchange molecular dynamics simulation. Chapter 5 describes an enhanced metric for convergence in parallel simulations called the normalized ergodic measure. The metric is applied to several properties for several replica exchange simulations. Advantages of this metric over other methods are described. Chapter 6 describes the implementation and optimization of an enhanced sampling algorithm similar to replica exchange molecular dynamics called multicanonical algorithm replica exchange molecular dynamics. The algorithm was implemented into a biomolecular simulation suite called AMBER. Additionally several parameters were analyzed and optimized. In Chapter 7, a pitfall in molecular dynamics is observed in biological systems that is caused by negligent use of a simulation's "thermostat". It was found that if the same pseudorandom number seed were used for multiple systems, they eventually synchronize. In this project, synchronization was observed in biological molecules. Various negative effects including corruption of data are pointed out. Chapter 8 describes molecular dynamics simulation of NikR, a homotetrameric nickel
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.
Integration methods for molecular dynamics
Leimkuhler, B.J.; Reich, S.; Skeel, R.D.
1996-12-31
Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplecticness, can be imposed on the discretization which tend to imply good long term behavior. The presence of a variety of types and strengths of interatom potentials in standard molecular models places severe restrictions on the timestep for numerical integration used in explicit integration schemes, so much recent research has concentrated on the search for alternatives that possess (1) proper dynamical properties, and (2) a relative insensitivity to the fastest components of the dynamics. We survey several recent approaches. 48 refs., 2 figs.
Examining the Mechanical Equilibrium of Microscopic Stresses in Molecular Simulations
NASA Astrophysics Data System (ADS)
Torres-Sánchez, Alejandro; Vanegas, Juan M.; Arroyo, Marino
2015-06-01
The microscopic stress field provides a unique connection between atomistic simulations and mechanics at the nanoscale. However, its definition remains ambiguous. Rather than a mere theoretical preoccupation, we show that this fact acutely manifests itself in local stress calculations of defective graphene, lipid bilayers, and fibrous proteins. We find that popular definitions of the microscopic stress violate the continuum statements of mechanical equilibrium, and we propose an unambiguous and physically sound definition.
Examining the Mechanical Equilibrium of Microscopic Stresses in Molecular Simulations.
Torres-Sánchez, Alejandro; Vanegas, Juan M; Arroyo, Marino
2015-06-26
The microscopic stress field provides a unique connection between atomistic simulations and mechanics at the nanoscale. However, its definition remains ambiguous. Rather than a mere theoretical preoccupation, we show that this fact acutely manifests itself in local stress calculations of defective graphene, lipid bilayers, and fibrous proteins. We find that popular definitions of the microscopic stress violate the continuum statements of mechanical equilibrium, and we propose an unambiguous and physically sound definition. PMID:26197144
Dynamical horizon entropy and equilibrium thermodynamics of generalized gravity theories
Wu Shaofeng; Ge Xianhui; Yang Guohong; Zhang Pengming
2010-02-15
We study the relation between the thermodynamics and field equations of generalized gravity theories on the dynamical trapping horizon with sphere symmetry. We assume the entropy of a dynamical horizon as the Noether charge associated with the Kodama vector and point out that it satisfies the second law when a Gibbs equation holds. We generalize two kinds of Gibbs equations to Gauss-Bonnet gravity on any trapping horizon. Based on the quasilocal gravitational energy found recently for f(R) gravity and scalar-tensor gravity in some special cases, we also build up the Gibbs equations, where the nonequilibrium entropy production, which is usually invoked to balance the energy conservation, is just absorbed into the modified Wald entropy in the Friedmann-Robertson-Walker spacetime with slowly varying horizon. Moreover, the equilibrium thermodynamic identity remains valid for f(R) gravity in a static spacetime. Our work provides an alternative treatment to reinterpret the nonequilibrium correction and supports the idea that the horizon thermodynamics is universal for generalized gravity theories.
Dynamics of Charged Particles in an Adiabatic Thermal Beam Equilibrium
NASA Astrophysics Data System (ADS)
Chen, Chiping; Wei, Haofei
2010-11-01
Charged-particle motion is studied in the self-electric and self-magnetic fields of a well-matched, intense charged-particle beam and an applied periodic solenoidal magnetic focusing field. The beam is assumed to be in a state of adiabatic thermal equilibrium. The phase space is analyzed and compared with that of the well-known Kapchinskij-Vladimirskij (KV)-type beam equilibrium. It is found that the widths of nonlinear resonances in the adiabatic thermal beam equilibrium are narrower than those in the KV-type beam equilibrium. Numerical evidence is presented, indicating almost complete elimination of chaotic particle motion in the adiabatic thermal beam equilibrium.
Molecular dynamics in high electric fields
NASA Astrophysics Data System (ADS)
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.
Molecular dynamics investigation of nanoscale cavitation dynamics
NASA Astrophysics Data System (ADS)
Sasikumar, Kiran; Keblinski, Pawel
2014-12-01
We use molecular dynamics simulations to investigate the cavitation dynamics around intensely heated solid nanoparticles immersed in a model Lennard-Jones fluid. Specifically, we study the temporal evolution of vapor nanobubbles that form around the solid nanoparticles heated over ps time scale and provide a detail description of the following vapor formation and collapse. For 8 nm diameter nanoparticles we observe the formation of vapor bubbles when the liquid temperature 0.5-1 nm away from the nanoparticle surface reaches ˜90% of the critical temperature, which is consistent with the onset of spinodal decomposition. The peak heat flux from the hot solid to the surrounding liquid at the bubble formation threshold is ˜20 times higher than the corresponding steady state critical heat flux. Detailed analysis of the bubble dynamics indicates adiabatic formation followed by an isothermal final stage of growth and isothermal collapse.
On calculating the equilibrium structure of molecular crystals.
Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene
2010-03-01
The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.
Collisional dynamics in a gas of molecular super-rotors.
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh
2015-01-01
Recently, 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 relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a 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 optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the 'gyroscopic stage' is abruptly terminated by an explosive rotational-translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules. PMID:26160223
Collisional dynamics in a gas of molecular super-rotors
NASA Astrophysics Data System (ADS)
Khodorkovsky, Yuri; Steinitz, Uri; Hartmann, Jean-Michel; Averbukh, Ilya Sh.
2015-07-01
Recently, 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 relatively slow. Here we study collisional equilibration dynamics of this new state of molecular gases. We show that the route to equilibrium starts with a 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 optical birefringence and anisotropic diffusion in the gas. After a certain induction time, the `gyroscopic stage' is abruptly terminated by an explosive rotational-translational energy exchange, leading the gas towards the final equilibrium. We illustrate our conclusions by direct molecular dynamics simulation of several gases of linear molecules.
Molecular Dynamics Simulation of Shock Induced Detonation
NASA Astrophysics Data System (ADS)
Tomar, Vikas; Zhou, Min
2004-07-01
This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.
Nonequilibrium molecular dynamics: The first 25 years
Hoover, W.G. |
1992-08-01
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.
Cell list algorithms for nonequilibrium molecular dynamics
NASA Astrophysics Data System (ADS)
Dobson, Matthew; Fox, Ian; Saracino, Alexandra
2016-06-01
We present two modifications of the standard cell list algorithm that handle molecular dynamics simulations with deforming periodic geometry. Such geometry naturally arises in the simulation of homogeneous, linear nonequilibrium flow modeled with periodic boundary conditions, and recent progress has been made developing boundary conditions suitable for general 3D flows of this type. Previous works focused on the planar flows handled by Lees-Edwards or Kraynik-Reinelt boundary conditions, while the new versions of the cell list algorithm presented here are formulated to handle the general 3D deforming simulation geometry. As in the case of equilibrium, for short-ranged pairwise interactions, the cell list algorithm reduces the computational complexity of the force computation from O(N2) to O(N), where N is the total number of particles in the simulation box. We include a comparison of the complexity and efficiency of the two proposed modifications of the standard algorithm.
Dielectrophoresis of nanocolloids: a molecular dynamics study.
Salonen, E; Terama, E; Vattulainen, I; Karttunen, M
2005-10-01
Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In this article we present, to our knowledge, the first molecular dynamics simulations of DEP of nanometer-sized colloidal particles. We introduce a simplified model for a polarizable nanoparticle, consisting of a large charged macroion and oppositely charged microions, in an explicit solvent. The model is then used to study DEP motion of the particle at different combinations of temperature and electric field strength. In accord with linear response theory, the particle drift velocities are shown to be proportional to the DEP force. Analysis of the colloid DEP mobility shows a clear time dependence, demonstrating the variation of friction under non-equilibrium. The time dependence of the mobility further results in an apparent weak variation of the DEP displacements with temperature. PMID:16195818
Non-equilibrium dynamics of ultracold atoms in optical lattices
NASA Astrophysics Data System (ADS)
Chen, David
This thesis describes experiments focused on investigating out-of-equilibrium phenomena in the Bose-Hubbard Model and exploring novel cooling techniques for ultracold gases in optical lattices. In the first experiment, we study quenches across the Mott-insulator-to-superfluid quantum phase transition in the 3D Bose-Hubbard Model. The quench is accomplished by continuously tuning the ratio of the Hubbard energies. We observe that the degree of excitation is proportional to the fraction of atoms that cross the phase boundary, and that the amount of excitations and energy produced during the quench have a power-law dependence on the quench rate. These phenomena suggest an excitation process analogous to the mechanism for defect generation in non-equilibrium classical phase transitions. This experiment constitutes the first observation of the Kibble-Zurek mechanism in a quantum quench. We have reported our findings in Ref. [1]. In a second experiment, published in Ref. [2], we investigate dissipation as a method for cooling a strongly interacting gas. We introduce dissipation via a bosonic reservoir to a strongly interacting bosonic gas in the Mott-insulator regime of a 3D spin-dependent optical lattice. The lattice atoms are excited to a higher energy band using laser-induced Bragg transitions. A weakly interacting superfluid comprised of atoms in a state that does not experience the lattice potential acts as a dissipative bath that interacts with the lattice atoms through collisions. We measure the resulting bath-induced decay using the atomic quasimomentum distribution, and we compare the decay rate with predictions from a weakly interacting model with no free parameters. A competing intrinsic decay mechanism arising from collisions between lattice atoms is also investigated. The presence of intrinsic decay can not be accommodated within a non-interacting framework and signals that strong interactions may play a central role in the lattice-atom dynamics. The
Fiftieth anniversary of molecular dynamics
NASA Astrophysics Data System (ADS)
Melker, Alexander I.
2007-04-01
The history of computer application in physics for solving nonlinear problems is considered. Examples from different branches of condensed matter physics (nonlinear vibrations of anharmonic chains of atoms, dynamics of radiation damage of crystals, deformation and fracture of crystals) are given. A new line of investigation and the results obtained in the field of computer simulation of physical processes realized in the department of metal physics and computer technologies in materials science are considered. This line incorporates both a study of self-organization and properties of new materials (fullerenes, carbon nanotubes) and biological objects by molecular dynamics technique as well as the development of new computer simulation methods.
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. PMID:27053964
Molecular dynamics on vector computers
NASA Astrophysics Data System (ADS)
Sullivan, F.; Mountain, R. D.; Oconnell, J.
1985-10-01
An algorithm called the method of lights (MOL) has been developed for the computerized simulation of molecular dynamics. The MOL, implemented on the CYBER 205 computer, is based on sorting and reformulating the manner in which neighbor lists are compiled, and it uses data structures compatible with specialized vector statements that perform parallel computations. The MOL is found to reduce running time over standard methods in scalar form, and vectorization is shown to produce an order-of-magnitude reduction in execution time.
Structure factor and rheology of chain molecules from molecular dynamics
NASA Astrophysics Data System (ADS)
Castrejón-González, Omar; Castillo-Tejas, Jorge; Manero, Octavio; Alvarado, Juan F. J.
2013-05-01
Equilibrium and non-equilibrium molecular dynamics were performed to determine the relationship between the static structure factor, the molecular conformation, and the rheological properties of chain molecules. A spring-monomer model with Finitely Extensible Nonlinear Elastic and Lennard-Jones force field potentials was used to describe chain molecules. The equations of motion were solved for shear flow with SLLOD equations of motion integrated with Verlet's algorithm. A multiple time scale algorithm extended to non-equilibrium situations was used as the integration method. Concentric circular patterns in the structure factor were obtained, indicating an isotropic Newtonian behavior. Under simple shear flow, some peaks in the structure factor were emerged corresponding to an anisotropic pattern as chains aligned along the flow direction. Pure chain molecules and chain molecules in solution displayed shear-thinning regions. Power-law and Carreau-Yasuda models were used to adjust the generated data. Results are in qualitative agreement with rheological and light scattering experiments.
Is the uptake of alcohols by H2O droplets governed by equilibrium solvation dynamics?
Taylor, R.S.; Dang, Liem, X.; Garret, B.C.
1997-12-31
Heterogeneous processes are important components of the earth`s atmospheric system. Experiments suggest that the interaction of small gas phase molecules with the liquid/vapor interface of aqueous droplets and their subsequent accommodation into the bulk of droplet is an integral part of these processes. A recently devised, molecular-level model predicts that this mass accommodation process is solely dependent on the rates of solvation and desorption of the impinging molecule and that the molecule must cross a large energy barrier before becoming solvated in the bulk water. In this work, we are using molecular dynamics computer simulations to examine this model. Due to the availability of experimental data, the ethanol-water and ethylene glycol-water systems have been chosen as prototypes for the mass accommodation process of non-reacting molecules. The potential of mean force technique is used to explore the equilibrium free energy surface for inserting these alcohols into bulk water from its vapor. These free energy profiles do not correspond to those predicted by the above mentioned model. The non-equilibrium aspects of this process are also explored.
Equilibrium analysis of the efficiency of an autonomous molecular computer
NASA Astrophysics Data System (ADS)
Rose, John A.; Deaton, Russell J.; Hagiya, Masami; Suyama, Akira
2002-02-01
In the whiplash polymerase chain reaction (WPCR), autonomous molecular computation is implemented in vitro by the recursive, self-directed polymerase extension of a mixture of DNA hairpins. Although computational efficiency is known to be reduced by a tendency for DNAs to self-inhibit by backhybridization, both the magnitude of this effect and its dependence on the reaction conditions have remained open questions. In this paper, the impact of backhybridization on WPCR efficiency is addressed by modeling the recursive extension of each strand as a Markov chain. The extension efficiency per effective polymerase-DNA encounter is then estimated within the framework of a statistical thermodynamic model. Model predictions are shown to provide close agreement with the premature halting of computation reported in a recent in vitro WPCR implementation, a particularly significant result, given that backhybridization had been discounted as the dominant error process. The scaling behavior further indicates completion times to be sufficiently long to render WPCR-based massive parallelism infeasible. A modified architecture, PNA-mediated WPCR (PWPCR) is then proposed in which the occupancy of backhybridized hairpins is reduced by targeted PNA2/DNA triplex formation. The efficiency of PWPCR is discussed using a modified form of the model developed for WPCR. Predictions indicate the PWPCR efficiency is sufficient to allow the implementation of autonomous molecular computation on a massive scale.
Gas adsorption and accumulation on hydrophobic surfaces: Molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Luo, Qing-Qun; Yang, Jie-Ming
2015-09-01
Molecular dynamics simulations show that the gas dissolved in water can be adsorbed at a hydrophobic interface and accumulates thereon. Initially, a water depletion layer appears on the hydrophobic interface. Gas molecules then enter the depletion layer and form a high-density gas-enriched layer. Finally, the gas-enriched layer accumulates to form a nanobubble. The radian of the nanobubble increases with time until equilibrium is reached. The equilibrium state arises through a Brenner-Lohse dynamic equilibrium mechanism, whereby the diffusive outflux is compensated by an influx near the contact line. Additionally, supersaturated gas also accumulates unsteadily in bulk water, since it can diffuse back into the water and is gradually adsorbed by a solid substrate. Project supported by the National Natural Science Foundation of China (Grant No. 21376161).
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
NASA Astrophysics Data System (ADS)
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to
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
2008-01-01
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 paper, 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. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper 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. PMID:16222654
Multisurface Adiabatic Reactive Molecular Dynamics.
Nagy, Tibor; Yosa Reyes, Juvenal; Meuwly, Markus
2014-04-01
Adiabatic reactive molecular dynamics (ARMD) simulation method is a surface-crossing algorithm for modeling chemical reactions in classical molecular dynamics simulations using empirical force fields. As the ARMD Hamiltonian is time dependent during crossing, it allows only approximate energy conservation. In the current work, the range of applicability of conventional ARMD is explored, and a new multisurface ARMD (MS-ARMD) method is presented, implemented in CHARMM and applied to the vibrationally induced photodissociation of sulfuric acid (H2SO4) in the gas phase. For this, an accurate global potential energy surface (PES) involving 12 H2SO4 and 4 H2O + SO3 force fields fitted to MP2/6-311G++(2d,2p) reference energies is employed. The MS-ARMD simulations conserve total energy and feature both intramolecular H-transfer reactions and water elimination. An analytical treatment of the dynamics in the crossing region finds that conventional ARMD can approximately conserve total energy for limiting cases. In one of them, the reduced mass of the system is large, which often occurs for simulations of solvated biomolecular systems. On the other hand, MS-ARMD is a general approach for modeling chemical reactions including gas-phase, homogeneous, heterogeneous, and enzymatic catalytic reactions while conserving total energy in atomistic simulations. PMID:26580356
Non-equilibrium transport in the quantum dot: quench dynamics and non-equilibrium steady state
NASA Astrophysics Data System (ADS)
Culver, Adrian; Andrei, Natan
We calculate the non-equilibrium current driven by a voltage drop across a quantum dot. The system is described by the two lead Anderson model at zero temperature with on-site Coulomb repulsion and non-interacting, linearized leads. We prepare the system in an initial state consisting of a free Fermi sea in each lead with the voltage drop given as the difference between the two Fermi levels. We quench the system by coupling the dot to the leads at t =0 and following the time evolution of the wavefunction. In the long time limit a new type of Bethe Ansatz wavefunction emerges, which satisfies the Lippmann-Schwinger equation with the two Fermi seas serving as the boundary conditions. The solution describes the non-equilibrium steady state of the system. We use this solution to compute the infinite time limit of the expectation value of the current operator at a given voltage, yielding the I-V characteristic. The calculation is non-perturbative and exact. Research supported by NSF Grant DMR 1410583.
Better, Cheaper, Faster Molecular Dynamics
NASA Technical Reports Server (NTRS)
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.
Molecular Dynamics Simulations of Polymers
NASA Astrophysics Data System (ADS)
Han, Jie
1995-01-01
Molecular dynamics (MD) simulations have been undertaken in this work to explore structures and properties of polyethylene (PE), polyisobutylene (PIB), atactic polypropylene (aPP) and atactic polystyrene (aPS). This work has not only demonstrated the reliability of MD simulations by comparing results with available experiments, but more importantly has revealed structure-property relationships on a molecular level for these selected polymers. Structures of these amorphous polymers were characterized by radial distribution functions (RDFs) or scattering profiles, and properties of the polymers studied were pressure-volume -temperature (PVT) equation of state, enthalpy, cohesive energy, the diffusion coefficient of methane in the polymer, and glass transition temperature. Good agreement was found for these structures and properties between simulation and experiment. More importantly, the scientific understanding of structure-property relationships was established on a molecular level. In the order of aPP (PE), PIB and aPS, with the chain surface separation or free volume decreasing, the density increases and the diffusion coefficient decreases. Therefore, the effects of changes or modifications in the chemical structure of monomer molecules (substituting pendent hydrogen with methyl or phenyl) on polymeric materials performance were attributed to the effects of molecular chain structure on packing structure, which, in turn, affects the properties of these polymers. Local chain dynamics and relaxation have been studied for bulk PE and aPS. Cooperative transitions occur at second-neighbor bonds for PE, and first-neighbor bonds for aPS due to the role of side groups. The activation energy is a single torsional barrier for overall conformational transitions, and is single torsional barrier plus locally "trapped" barrier for relaxation. Temperature dependence is Arrhenius for transition time, and is WLF for relaxation time. The mean correlation times derived from
Studying non-equilibrium many-body dynamics using one-dimensional Bose gases
Langen, Tim; Gring, Michael; Kuhnert, Maximilian; Rauer, Bernhard; Geiger, Remi; Mazets, Igor; Smith, David Adu; Schmiedmayer, Jörg; Kitagawa, Takuya; Demler, Eugene
2014-12-04
Non-equilibrium dynamics of isolated quantum many-body systems play an important role in many areas of physics. However, a general answer to the question of how these systems relax is still lacking. We experimentally study the dynamics of ultracold one-dimensional (1D) Bose gases. This reveals the existence of a quasi-steady prethermalized state which differs significantly from the thermal equilibrium of the system. Our results demonstrate that the dynamics of non-equilibrium quantum many-body systems is a far richer process than has been assumed in the past.
Dynamics of dewetting at the nanoscale using molecular dynamics.
Bertrand, E; Blake, T D; Ledauphin, V; Ogonowski, G; Coninck, J De; Fornasiero, D; Ralston, J
2007-03-27
Large-scale molecular dynamics simulations are used to model the dewetting of solid surfaces by partially wetting thin liquid films. Two levels of solid-liquid interaction are considered that give rise to large equilibrium contact angles. The initial length and thickness of the films are varied over a wide range at the nanoscale. Spontaneous dewetting is initiated by removing a band of molecules either from each end of the film or from its center. As observed experimentally and in previous simulations, the films recede at an initially constant speed, creating a growing rim of liquid with a constant receding dynamic contact angle. Consistent with the current understanding of wetting dynamics, film recession is faster on the more poorly wetted surface to an extent that cannot be explained solely by the increase in the surface tension driving force. In addition, the rates of recession of the thinnest films are found to increase with decreasing film thickness. These new results imply not only that the mobility of the liquid molecules adjacent to the solid increases with decreasing solid-liquid interactions, but also that the mobility adjacent to the free surface of the film is higher than in the bulk, so that the effective viscosity of the film decreases with thickness. PMID:17328565
Molecular dynamics modeling of a nanomaterials-water surface interaction
NASA Astrophysics Data System (ADS)
Nejat Pishkenari, Hossein; Keramati, Ramtin; Abdi, Ahmad; Minary-Jolandan, Majid
2016-04-01
In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements.
ERIC Educational Resources Information Center
Chiu, Mei-Hung; Chou, Chin-Cheng; Liu, Chia-Ju
2002-01-01
Investigates students' mental models of chemical equilibrium using dynamic science assessments. Reports that students at various levels have misconceptions about chemical equilibrium. Involves 10th grade students (n=30) in the study doing a series of hands-on chemical experiments. Focuses on the process of constructing mental models, dynamic…
Molecular dynamics simulations of microscale fluid transport
Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.
1998-02-01
Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.
The "Collisions Cube" Molecular Dynamics Simulator.
ERIC Educational Resources Information Center
Nash, John J.; Smith, Paul E.
1995-01-01
Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)
Tassis, Konstantinos; Willacy, Karen; Yorke, Harold W.; Turner, Neal J.
2012-07-20
We study the effect that non-equilibrium chemistry in dynamical models of collapsing molecular cloud cores has on measurements of the magnetic field in these cores, the degree of ionization, and the mean molecular weight of ions. We find that OH and CN, usually used in Zeeman observations of the line-of-sight magnetic field, have an abundance that decreases toward the center of the core much faster than the density increases. As a result, Zeeman observations tend to sample the outer layers of the core and consistently underestimate the core magnetic field. The degree of ionization follows a complicated dependence on the number density at central densities up to 10{sup 5} cm{sup -3} for magnetic models and 10{sup 6} cm{sup -3} in non-magnetic models. At higher central densities, the scaling approaches a power law with a slope of -0.6 and a normalization which depends on the cosmic-ray ionization rate {zeta} and the temperature T as ({zeta}T){sup 1/2}. The mean molecular weight of ions is systematically lower than the usually assumed value of 20-30, and, at high densities, approaches a value of 3 due to the asymptotic dominance of the H{sup +}{sub 3} ion. This significantly lower value implies that ambipolar diffusion operates faster.
Osmosis : a molecular dynamics computer simulation study
NASA Astrophysics Data System (ADS)
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..
NASA Astrophysics Data System (ADS)
Sarychev, V. A.; Gutnik, S. A.
2015-11-01
The rotational dynamics of a satellite moving over a circular orbit under an effect of gravitational and aerodynamic torques is investigated. A method is proposed for determining all equilibrium positions (equilibrium orientations) of a satellite in an orbital coordinate system with given values of an aerodynamic torque vector and principal central moments of inertia; the conditions of their existence are obtained, depending on four dimensionless parameters of the problem. Bifurcation values of parameters are found for which the number of equilibrium orientations changes. The numerical analysis of the evolution of regions of existence of various numbers of equilibrium orientations in the space of dimensionless parameters is carried out. The relationship between the obtained regions of existence and the regions of existence of equilibrium orientations of an axisymmetric satellite is considered. It is shown that the number of equilibrium positions of a satellite does not exceed 24 and cannot be less than 8, in the general case.
Nonadiabatic Molecular Dynamics with Trajectories
NASA Astrophysics Data System (ADS)
Tavernelli, Ivano
2012-02-01
In the mixed quantum-classical description of molecular systems, only the quantum character of the electronic degrees of freedom is considered while the nuclear motion is treated at a classical level. In the adiabatic case, this picture corresponds to the Born-Oppenheimer limit where the nuclei move as point charges on the potential energy surface (PES) associated with a given electronic state. Despite the success of this approximation, many physical and chemical processes do not fall in the regime where nuclei and electrons can be considered decoupled. In particular, most photoreactions pass through regions of the PES in which electron-nuclear quantum interference effects are sizeable and often crucial for a correct description of the phenomena. Recently, we have developed a trajectory-based nonadiabatic molecular dynamics scheme that describes the nuclear wavepacket as an ensemble of particles following classical trajectories on PESs derived from time-dependent density functional theory (TDDFT) [1]. The method is based on Tully's fewest switches trajectories surface hopping (TSH) where the nonadiabatic coupling elements between the different potential energy surfaces are computed on-the-fly as functionals of the ground state electron density or, equivalently, of the corresponding Kohn-Sham orbitals [2]. Here, we present the theoretical fundamentals of our approach together with an extension that allows for the direct coupling of the dynamics to an external electromagnetic field [3] as well as to the external potential generated by the environment (solvent effects) [4]. The method is applied to the study of the photodissociation dynamics of simple molecules in gas phase and to the description of the fast excited state dynamics of molecules in solution (in particular Ruthenium (II) tris(bipyridine) in water). [4pt] [1] E. Tapavicza, I. Tavernelli, U. Rothlisberger, Phys. Rev. Lett., 98, (2007) 023001. [0pt] [2] Tavernelli I.; Tapavicza E.; Rothlisberger U., J. Chem
Molecular dynamics simulation of benzene
NASA Astrophysics Data System (ADS)
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.
Buckybomb: Reactive Molecular Dynamics Simulation.
Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V
2015-03-01
Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672
NASA Astrophysics Data System (ADS)
Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.
2016-04-01
The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited state molecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited state molecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission.
NASA Astrophysics Data System (ADS)
Jing, Yuanyuan; Chen, Liping; Bai, Shuming; Shi, Qiang
2013-01-01
The hierarchical equations of motion (HEOM) method was applied to calculate the emission spectra of molecular aggregates using the Frenkel exciton model. HEOM equations for the one-exciton excited state were first propagated until equilibration. The reduced density operator and auxiliary density operators (ADOs) were used to characterize the coupled system-bath equilibrium. The dipole-dipole correlation functions were then calculated to obtain the emission spectra of model dimers, and the B850 band of light-harvesting complex II (LH2) in purple bacteria. The effect of static disorder on equilibrium excited state and the emission spectra of LH2 was also explicitly considered. Several approximation schemes, including the high temperature approximation (HTA) of the HEOM, a modified version of the HTA, the stochastic Liouville equation approach, the perturbative time-local and time-nonlocal generalized quantum master equations, were assessed in the calculation of the equilibrium excited state and emission spectra.
Molecular dynamics studies on nanoscale gas transport
NASA Astrophysics Data System (ADS)
Barisik, Murat
Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the
Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms
Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R
2005-02-02
Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.
Equilibrium and non-equilibrium dynamics of the dilute lamellar phase
NASA Astrophysics Data System (ADS)
Ramaswamy, Sriram
1992-07-01
A model for the dynamics of the sterically stabilized dilute lamellar phase is constructed and studied. The model consists of a stack of flexible fluid sheets, with excluded volume, separated by macroscopic layers of solvent. The dynamics of small fluctuations of the sheets about their mean positions is found to have two distinct short-wavelength regimes in which the frequency ω depends on the wavenumber q in an unusual manner. One is a single-membrane Zimm mode, ω ≈ - iq3, while the other is a “red-blood-cell mode”, ω ≈ - iq6. These modes give rise to fluctuation corrections for the viscosities of the system, going as ω {-1}/{3} and ω {-2}/{3}, respectively. In addition, it is shown that a sufficiently rapid shear flow with velocity and gradient in the plane of the layers causes a transition into a state where regions of reduced layer spacing co-exist with regions devoid of any layer material. The critical shear-rate for this transition should go as (layer spacing) -3. Possible experimental tests of these predictions are discussed.
Molecular dynamics of membrane proteins.
Woolf, Thomas B.; 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.
Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics
NASA Astrophysics Data System (ADS)
Rakesh, L.
2009-09-01
Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the
Non-equilibrium dynamics of glass-forming liquid mixtures
NASA Astrophysics Data System (ADS)
Sánchez-Díaz, Luis Enrique; Lázaro-Lázaro, Edilio; Olais-Govea, José Manuel; Medina-Noyola, Magdaleno
2014-06-01
The non-equilibrium self-consistent generalized Langevin equation theory of irreversible processes in glass-forming liquids [P. Ramírez-González and M. Medina-Noyola, Phys. Rev. E 82, 061503 (2010)] is extended here to multi-component systems. The resulting theory describes the statistical properties of the instantaneous local particle concentration profiles nα(r, t) of species α in terms of the coupled time-evolution equations for the mean value overline{n}_α ({r},t) and for the covariance σ _{α β }({r},{r}^' };t)equiv overline{δ n_α ({r},t)δ n_β ({r}^' },t)} of the fluctuations δ n_α ({r},t) = n_α ({r},t)- overline{n}_α ({r},t). As in the monocomponent case, these two coarse-grained equations involve a local mobility function bα(r, t) for each species, written in terms of the memory function of the two-time correlation function C_{α β }({r},{r}^' };t,t^' }) equiv overline{δ n_α ({r},t)δ n_β ({r}^' },t^' })}. If the system is constrained to remain spatially uniform and subjected to a non-equilibrium preparation protocol described by a given temperature and composition change program T(t) and overline{n}_α (t), these equations predict the irreversible structural relaxation of the partial static structure factors Sαβ(k; t) and of the (collective and self) intermediate scattering functions Fαβ(k, τ; t) and F^S_{α β }(k,τ ;t). We illustrate the applicability of the resulting theory with two examples involving simple model mixtures subjected to an instantaneous temperature quench: an electroneutral binary mixture of equally sized and oppositely charged hard-spheres, and a binary mixture of soft-spheres of moderate size-asymmetry.
Langevin stabilization of molecular dynamics
NASA Astrophysics Data System (ADS)
Izaguirre, Jesús A.; Catarello, Daniel P.; Wozniak, Justin M.; Skeel, Robert D.
2001-02-01
In this paper we show the possibility of using very mild stochastic damping to stabilize long time step integrators for Newtonian molecular dynamics. More specifically, stable and accurate integrations are obtained for damping coefficients that are only a few percent of the natural decay rate of processes of interest, such as the velocity autocorrelation function. Two new multiple time stepping integrators, Langevin Molly (LM) and Brünger-Brooks-Karplus-Molly (BBK-M), are introduced in this paper. Both use the mollified impulse method for the Newtonian term. LM uses a discretization of the Langevin equation that is exact for the constant force, and BBK-M uses the popular Brünger-Brooks-Karplus integrator (BBK). These integrators, along with an extrapolative method called LN, are evaluated across a wide range of damping coefficient values. When large damping coefficients are used, as one would for the implicit modeling of solvent molecules, the method LN is superior, with LM closely following. However, with mild damping of 0.2 ps-1, LM produces the best results, allowing long time steps of 14 fs in simulations containing explicitly modeled flexible water. With BBK-M and the same damping coefficient, time steps of 12 fs are possible for the same system. Similar results are obtained for a solvated protein-DNA simulation of estrogen receptor ER with estrogen response element ERE. A parallel version of BBK-M runs nearly three times faster than the Verlet-I/r-RESPA (reversible reference system propagator algorithm) when using the largest stable time step on each one, and it also parallelizes well. The computation of diffusion coefficients for flexible water and ER/ERE shows that when mild damping of up to 0.2 ps-1 is used the dynamics are not significantly distorted.
Predicting long-term and short-term tidal flat morphodynamics using a dynamic equilibrium theory
NASA Astrophysics Data System (ADS)
Hu, Zhan; Wang, Zheng Bing; Zitman, Tjerk J.; Stive, Marcel J. F.; Bouma, Tjeerd J.
2015-09-01
Dynamic equilibrium theory is a fruitful concept, which we use to systematically explain the tidal flat morphodynamic response to tidal currents, wind waves, sediment supply, and other sedimentological drivers. This theory stems from a simple analytical model that derives the tide- or wave-dominated tidal flat morphology by assuming that morphological equilibrium is associated with uniform bed shear stress distribution. Many studies based on observation and process-based modeling tend to agree with this analytical model. However, a uniform bed shear stress rarely exists on actual or modeled tidal flats, and the analytical model cannot handle the spatially and temporally varying bed shear stress. In the present study, we develop a model based on the dynamic equilibrium theory and its core assumption. Different from the static analytical model, our model explicitly accounts for the spatiotemporal bed shear stress variations for tidal flat dynamic prediction. To test our model and the embedded theory, we apply the model for both long-term and short-term morphological predictions. The long-term modeling is evaluated qualitatively against previous process-based modeling. The short-term modeling is evaluated quantitatively against high-resolution bed-level monitoring data obtained from a tidal flat in Netherlands. The model results show good performances in both qualitative and quantitative tests, indicating the validity of the dynamic equilibrium theory. Thus, this model provides a valuable tool to enhance our understanding of the tidal flat morphodynamics and to apply the dynamic equilibrium theory for realistic morphological predictions.
Imaging the equilibrium state and magnetization dynamics of partially built hard disk write heads
Valkass, R. A. J. Yu, W.; Shelford, L. R.; Keatley, P. S.; Loughran, T. H. J.; Hicken, R. J.; Cavill, S. A.; Laan, G. van der; Dhesi, S. S.; Bashir, M. A.; Gubbins, M. A.; Czoschke, P. J.; Lopusnik, R.
2015-06-08
Four different designs of partially built hard disk write heads with a yoke comprising four repeats of NiFe (1 nm)/CoFe (50 nm) were studied by both x-ray photoemission electron microscopy (XPEEM) and time-resolved scanning Kerr microscopy (TRSKM). These techniques were used to investigate the static equilibrium domain configuration and the magnetodynamic response across the entire structure, respectively. Simulations and previous TRSKM studies have made proposals for the equilibrium domain configuration of similar structures, but no direct observation of the equilibrium state of the writers has yet been made. In this study, static XPEEM images of the equilibrium state of writer structures were acquired using x-ray magnetic circular dichroism as the contrast mechanism. These images suggest that the crystalline anisotropy dominates the equilibrium state domain configuration, but competition with shape anisotropy ultimately determines the stability of the equilibrium state. Dynamic TRSKM images were acquired from nominally identical devices. These images suggest that a longer confluence region may hinder flux conduction from the yoke into the pole tip: the shorter confluence region exhibits clear flux beaming along the symmetry axis, whereas the longer confluence region causes flux to conduct along one edge of the writer. The observed variations in dynamic response agree well with the differences in the equilibrium magnetization configuration visible in the XPEEM images, confirming that minor variations in the geometric design of the writer structure can have significant effects on the process of flux beaming.
Near-equilibrium polymorphic phase transformations in Praseodymium under dynamic compression
Bastea, M; Reisman, D
2007-02-12
We report the first experimental observation of sequential, multiple polymorphic phase transformations occurring in Praseodymium dynamically compressed using a ramp wave. The experiments also display the signatures of reverse transformations occuring upon pressure release and reveal the presence of small hysteresys loops. The results are in very good agreement with equilibrium hydrodynamic calculations performed using a thermodynamically consistent, multi-phase equation of state for Praseodymium, suggesting a near-equilibrium transformation behavior.
Dynamical Localization in Molecular Systems.
NASA Astrophysics Data System (ADS)
Wang, Xidi
In the first four chapters of this thesis we concentrate on the Davydov model which describes the vibrational energy quanta of Amide I bonds (C=O bonds on the alpha -helix) coupled to the acoustic phonon modes of the alpha-helix backbone in the form of a Frohlich Hamiltonian. Following a brief introduction in chapter one, in chapter two we formulate the dynamics of vibrational quanta at finite temperature by using coherent state products. The fluctuation-dissipation relation is derived. At zero temperature, in the continuum limit, we recover the original results of Davydov. We also achieve good agreement with numerical simulations. In chapter three, the net contraction of the lattice is calculated exactly at any temperature, and its relation to the so -call "topological stability" of the Davydov soliton is discussed. In the second section of the chapter three we calculate the overtone spectra of crystalline acetanilide (according to some opinions ACN provides experimental evidence for the existence of Davydov solitons). Good agreement with experimental data has been obtained. In chapter four we study the self-trapped vibrational excitations by the Quantum Monte Carlo technique. For a single excitation, the temperature dependence of different physical observables is calculated. The quasi-particle which resembles the Davydov soliton has been found to be fairly narrow using the most commonly used data for the alpha -helix; at temperatures above a few Kelvin, the quasi-particle reaches its smallest limit (extends over three sites), which implies diffusive motion of the small polaron-like quasi-particle at high temperatures. For the multi-excitation case, bound pairs and clusters of excitations are found at low temperatures; they gradually dissociate when the temperature of the system is increased as calculated from the density-density correlation function. In the last chapter of this thesis, we study a more general model of dynamical local modes in molecular systems
NASA Astrophysics Data System (ADS)
Barone, Luciano Maria; Simonazzi, Riccardo; Tenenbaum, Alexander
1995-09-01
We have studied portability, efficiency and accuracy of a standard Molecular Dynamics simulation on the SIMD parallel computer APE100. Computing speed performance and physical system size range have been analyzed and compared with those of a conventional computer. Short range and long range potentials have been considered, and the comparative advantage of different simulation approaches has been assessed. For long range potentials, APE turns out to be faster than a conventional computer; large systems can be conveniently simulated using either the cloning approach (up to ˜ 10 5 particles) or a domain decomposition with the systolic method. In the case of short range potentials and systems with diffusion (like a liquid), APE is convenient only when using a large number of processors. In a special case (a crystal without diffusion), a specific domain decomposition technique with frames makes APE advantageous for intermediate and large systems. Using the latter technique we have studied in detail the effect of different numerical error sources, and compared the accuracy of APE with that of a conventional computer.
Dynamics of riboswitches: Molecular simulations.
Sanbonmatsu, Karissa Y
2014-10-01
Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail. Molecular dynamics simulations are useful for interpreting existing experimental data and producing predictions for new experiments. Here, a wide range of computational studies on riboswitches is reviewed. By elucidating the key principles of riboswitch operation, computation may aid in the effort to design more specific antibiotics with affinities greater than those of the native ligand. Such a detailed understanding may be required to improve efficacy and reduce side effects. These studies are laying the groundwork for understanding the action mechanism of new compounds that inhibit riboswitch activity. Future directions such as magnesium effects, large-scale conformational changes, expression platforms and co-transcriptional folding are also discussed. This article is part of a Special Issue entitled: Riboswitches. PMID:24953187
Relaxation to equilibrium driven via indirect control in Markovian dynamics
Romano, Raffaele
2007-11-15
We prove that it is possible to modify the stationary states of a quantum dynamical semigroup, describing the irreversible evolution of a two-level system, by means of an auxiliary two-level system, a quantum probe that can be suitably prepared. The target system and the probe can be initially entangled or uncorrelated. We find that this indirect control of the stationary states is possible, even if there are no initial correlations, under suitable conditions on the dynamical parameters characterizing the evolution of the joint system.
Non-equilibrium dynamics of glass-forming liquid mixtures
Sánchez-Díaz, Luis Enrique; Lázaro-Lázaro, Edilio; Olais-Govea, José Manuel; Medina-Noyola, Magdaleno
2014-06-21
The non-equilibrium self-consistent generalized Langevin equation theory of irreversible processes in glass-forming liquids [P. Ramírez-González and M. Medina-Noyola, Phys. Rev. E 82, 061503 (2010)] is extended here to multi-component systems. The resulting theory describes the statistical properties of the instantaneous local particle concentration profiles n{sub α}(r, t) of species α in terms of the coupled time-evolution equations for the mean value n{sup ¯}{sub α}(r,t) and for the covariance σ{sub αβ}(r,r{sup ′};t)≡δn{sub α}(r,t)δn{sub β}(r{sup ′},t){sup ¯} of the fluctuations δn{sub α}(r,t)=n{sub α}(r,t)−n{sup ¯}{sub α}(r,t). As in the monocomponent case, these two coarse-grained equations involve a local mobility function b{sub α}(r, t) for each species, written in terms of the memory function of the two-time correlation function C{sub αβ}(r,r{sup ′};t,t{sup ′})≡δn{sub α}(r,t)δn{sub β}(r{sup ′},t{sup ′}){sup ¯}. If the system is constrained to remain spatially uniform and subjected to a non-equilibrium preparation protocol described by a given temperature and composition change program T(t) and n{sup ¯}{sub α}(t), these equations predict the irreversible structural relaxation of the partial static structure factors S{sub αβ}(k; t) and of the (collective and self) intermediate scattering functions F{sub αβ}(k, τ; t) and F{sub αβ}{sup S}(k,τ;t). We illustrate the applicability of the resulting theory with two examples involving simple model mixtures subjected to an instantaneous temperature quench: an electroneutral binary mixture of equally sized and oppositely charged hard-spheres, and a binary mixture of soft-spheres of moderate size-asymmetry.
Dynamic non-equilibrium wall-modeling for large eddy simulation at high Reynolds numbers
NASA Astrophysics Data System (ADS)
Kawai, Soshi; Larsson, Johan
2013-01-01
A dynamic non-equilibrium wall-model for large-eddy simulation at arbitrarily high Reynolds numbers is proposed and validated on equilibrium boundary layers and a non-equilibrium shock/boundary-layer interaction problem. The proposed method builds on the prior non-equilibrium wall-models of Balaras et al. [AIAA J. 34, 1111-1119 (1996)], 10.2514/3.13200 and Wang and Moin [Phys. Fluids 14, 2043-2051 (2002)], 10.1063/1.1476668: the failure of these wall-models to accurately predict the skin friction in equilibrium boundary layers is shown and analyzed, and an improved wall-model that solves this issue is proposed. The improvement stems directly from reasoning about how the turbulence length scale changes with wall distance in the inertial sublayer, the grid resolution, and the resolution-characteristics of numerical methods. The proposed model yields accurate resolved turbulence, both in terms of structure and statistics for both the equilibrium and non-equilibrium flows without the use of ad hoc corrections. Crucially, the model accurately predicts the skin friction, something that existing non-equilibrium wall-models fail to do robustly.
Non-Equilibrium Dynamics of Nano-channel Confined DNA: A Brownian Dynamics Simulation Study
NASA Astrophysics Data System (ADS)
Bhattacharya, Aniket; Huang, Aiqun; Reisner, Walter
We carry out Brownian dynamics (BD) simulation for a semi-flexible polymer chain characterized by a contour length Na and a persistence length lp confined inside a rectangular nanochannel to study its compression and retraction dynamics while being pushed on one end at a constant velocity by a ``nano-dozer''. We study the evolution of one dimensional concentration profile c (x , t) and the chain extension R along the channel axis (x-axis) during both the contracting as well as the retracting phases as a function of the velocity of the nano-dozer, both in steady states and in transients. Furthermore, we measure the transverse fluctuations of the chain under contraction and retraction, and the amplitude of the density profile, and compare these simulation results with those obtained from an analytical model proposed by Khorshid et al. Our studies are guided by recent experimental results by Khorshid et al. (Phys. Rev. Lett, 113, 268104 (2014)) and provide further justification to use a one dimensional PDE approach to understand the non-equilibrium dynamics of confined polymers.
Universal far-from-equilibrium dynamics of a holographic superconductor.
Sonner, Julian; Del Campo, Adolfo; Zurek, Wojciech H
2015-01-01
Symmetry-breaking phase transitions are an example of non-equilibrium processes that require real-time treatment, a major challenge in strongly coupled systems without long-lived quasiparticles. Holographic duality provides such an approach by mapping strongly coupled field theories in D dimensions into weakly coupled quantum gravity in D+1 anti-de Sitter spacetime. Here we use holographic duality to study the formation of topological defects-winding numbers-in the course of a superconducting transition in a strongly coupled theory in a 1D ring. When the system undergoes the transition on a given quench time, the condensate builds up with a delay that can be deduced using the Kibble-Zurek mechanism from the quench time and the universality class of the theory, as determined from the quasinormal mode spectrum of the dual model. Typical winding numbers deposited in the ring exhibit a universal fractional power law dependence on the quench time, also predicted by the Kibble-Zurek Mechanism. PMID:26100330
Extremely far from equilibrium: the multiscale dynamics of streamers
NASA Astrophysics Data System (ADS)
Ebert, Ute
2012-10-01
Streamers can emerge when high voltages are applied to gases. At their tips, the electric field is strongly enhanced, and electron energies locally reach distributions very far from equilibrium, with long tails at high energies. These exotic electron energies create radiation and chemical excitations at very low energy input, as the gas stays cold while the ionization front passes. Applications are multiple: highly efficient O* radical production in air for disinfection, combustion gas cleaning, plasma assisted combustion, plasma bullets in medicine etc. In that sense, streamers can be considered as very efficient converters of pulsed electric into chemical energy, in particular, if the electric circuits are optimized for the application. Streamers are also ubiquitous in nature, e.g., in the streamer corona of lightning leaders, in sprite discharges high above the clouds; and streamers also seem to contribute to generating gamma-ray flashes and even to electron-positron beams in active thunderstorms. Unravelling the intrinsic mechanisms of streamers is challenging: they can move with up to one tenth of the speed of light, and they have an intricate nonlinear structure with a hierarchy of scales. I will review how theory and experiment deal with these structures, and I will discuss the basic differences between positive and negative streamers, electron acceleration at streamer tips and the consecutive radiation and chemical reactions, the propagation mechanism of positive streamers in different gases, streamer velocities and diameters varying over at least two orders of magnitude, streamer branching and interaction, and their three-dimensional tree structure. Both theory and experiment work with a patchwork of methods, and geophysics can provide movies that cannot be taken in the lab. I will sketch the state and outline open questions.
NASA Astrophysics Data System (ADS)
Chiu, Mei-Hung; Chou, Chin-Cheng; Liu, Chia-Ju
2002-10-01
The purpose of this study was to investigate students' mental models of chemical equilibrium using dynamic science assessments. Research in chemical education has shown that students at various levels have misconceptions about chemical equilibrium. According to Chi's theory of conceptual change, the concept of chemical equilibrium has constraint-based features (e.g., random, simultaneous, uniform activities) that might prevent students from deeply understanding the nature of the concept of chemical equilibrium. In this study, we examined how students learned and constructed their mental models of chemical equilibrium in a cognitive apprenticeship context. Thirty 10th-grade students participated in the study: 10 in a control group and 20 in a treatment group. Both groups were presented with a series of hands-on chemical experiments. The students in the treatment group were instructed based on the main features of cognitive apprenticeship (CA), such as coaching, modeling, scaffolding, articulation, reflection, and exploration. However, the students in the control group (non-CA group) learned from the tutor without explicit CA support. The results revealed that the CA group significantly outperformed the non-CA group. The students in the CA group were capable of constructing the mental models of chemical equilibrium - including dynamic, random activities of molecules and interactions between molecules in the microworld - whereas the students in the non-CA group failed to construct similar correct mental models of chemical equilibrium. The study focuses on the process of constructing mental models, on dynamic changes, and on the actions of students (such as self-monitoring/self-correction) who are learning the concept of chemical equilibrium. Also, we discuss the implications for science education.
Out of equilibrium energy dynamics in low dimensional quantum magnets
NASA Astrophysics Data System (ADS)
Langer, Stephan; Heyl, Markus; McCulloch, Ian; Heidrich-Meisner, Fabian
2012-02-01
We investigate the real-time dynamics of the energy density in spin-1/2 XXZ chains using two types of quenches resulting in initial states which feature an inhomogeneous distribution of local energies [1]. The first involves quenching bonds in the center of the chain from antiferromagnetic to ferromagnetic exchange interactions. The second quench involves an inhomogeneous magnetic field, inducing both, an inhomogeneous magnetization profile [2] and local energy density. The simulations are carried out using the adaptive time-dependent density matrix renormalization group algorithm. We analyze the time-dependence of the spatial variance of the bond energies and the local energy currents which both yield necessary criteria for ballistic or diffusive energy dynamics. For both setups, our results are consistent with ballistic behavior, both in the massless and the massive phase. For the massless regime, we compare our numerical results to bosonization and the non-interacting limit finding very good agreement. The velocity of the energy wave-packets can be understood as the average velocity of excitations induced by the quench. [4pt] [1] Langer et al. Phys. Rev. B in press; arXiv:1107.4136[0pt] [2] Langer et al. Phys. Rev. B 79, 214409 (2009)
Time-Dependent Molecular Reaction Dynamics
Oehrn, Yngve
2007-11-29
This paper is a brief review of a time-dependent, direct, nonadiabatic theory of molecular processes called Electron Nuclear Dynamics (END). This approach to the study of molecular reaction dynamics is a hierarchical theory that can be applied at various levels of approximation. The simplest level of END uses classical nuclei and represents all electrons by a single, complex, determinantal wave function. The wave function parameters such as average nuclear positions and momenta, and molecular orbital coefcients carry the time dependence and serve as dynamical variables. Examples of application are given of the simplest level of END to ion-atom and ion-molecule reactions.
Non-equilibrium dynamics contribute to ion selectivity in the KcsA channel.
Ngo, Van; Stefanovski, Darko; Haas, Stephan; Farley, Robert A
2014-01-01
The ability of biological ion channels to conduct selected ions across cell membranes is critical for the survival of both animal and bacterial cells. Numerous investigations of ion selectivity have been conducted over more than 50 years, yet the mechanisms whereby the channels select certain ions and reject others are not well understood. Here we report a new application of Jarzynski's Equality to investigate the mechanism of ion selectivity using non-equilibrium molecular dynamics simulations of Na(+) and K(+) ions moving through the KcsA channel. The simulations show that the selectivity filter of KcsA adapts and responds to the presence of the ions with structural rearrangements that are different for Na(+) and K(+). These structural rearrangements facilitate entry of K(+) ions into the selectivity filter and permeation through the channel, and rejection of Na(+) ions. A mechanistic model of ion selectivity by this channel based on the results of the simulations relates the structural rearrangement of the selectivity filter to the differential dehydration of ions and multiple-ion occupancy and describes a mechanism to efficiently select and conduct K(+). Estimates of the K(+)/Na(+) selectivity ratio and steady state ion conductance for KcsA from the simulations are in good quantitative agreement with experimental measurements. This model also accurately describes experimental observations of channel block by cytoplasmic Na(+) ions, the "punch through" relief of channel block by cytoplasmic positive voltages, and is consistent with the knock-on mechanism of ion permeation. PMID:24465882
Entangled polymer dynamics in equilibrium and flow modeled through slip links.
Schieber, Jay D; Andreev, Marat
2014-01-01
The idea that the dynamics of concentrated, high-molecular weight polymers are largely governed by entanglements is now widely accepted and typically understood through the tube model. Here we review alternative approaches, slip-link models, that share some similarities to and offer some advantages over tube models. Although slip links were proposed at the same time as tubes, only recently have detailed, quantitative mathematical models arisen based on this picture. In this review, we focus on these models, with most discussion limited to mathematically well-defined objects that conform to state-of-the-art beyond-equilibrium thermodynamics. These models are connected to each other through successive coarse graining, using nonequilibrium thermodynamics along the way, and with a minimal parameter set. In particular, the most detailed level of description has four parameters, three of which can be determined directly from atomistic simulations. Once the remaining parameter is determined for any system, all parameters for all members of the hierarchy are determined. We show how, using this hierarchy of slip-link models combined with atomistic simulations, we can make predictions about the nonlinear rheology of monodisperse homopolymer melts, polydisperse melts, or blends of different architectures. Mathematical details are given elsewhere, so these are limited here, and physical ideas are emphasized. We conclude with an outlook on remaining challenges that might be tackled successfully using this approach, including complex flow fields and polymer blends. PMID:24655135
Non-equilibrium Dynamics of an Optomechanical Dicke Model
NASA Astrophysics Data System (ADS)
Kamanasish, Debnath; Aranya, B. Bhattacherjee
2015-07-01
Motivated by the experimental realization of Dicke model in optical cavities, we model an optomechanical system consisting of two-level BEC atoms with transverse pumping. We investigate the transition from normal and inverted state to the superradiant phase through a detailed study of the phase portraits of the system. The rich phase portraits generated by analytical arguments display two types of superradiant phases, regions of coexistence and some portion determining the persistent oscillations. We study the time evolution of the system from any phase and discuss the role of mirror frequency in reaching their attractors. Further, we add an external mechanical pump to the mirror which is capable of changing the mirror frequency through radiation pressure and study the impact of the pump on the phase portraits and the dynamics of the system. We find the external mirror frequency changing the phase portraits and even shifting the critical transition point, thereby predicting a system with controllable phase transition.
Dynamic vacuum variable and equilibrium approach in cosmology
Klinkhamer, F. R.; Volovik, G. E.
2008-09-15
A modified-gravity theory is considered with a four-form field strength F, a variable gravitational coupling parameter G(F), and a standard matter action. This theory provides a concrete realization of the general vacuum variable q as the four-form amplitude F and allows for a study of its dynamics. The theory gives a flat Friedmann-Robertson-Walker universe with rapid oscillations of the effective vacuum energy density (cosmological ''constant''), whose amplitude drops to zero asymptotically. Extrapolating to the present age of the Universe, the order of magnitude of the average vacuum energy density agrees with the observed near-critical vacuum energy density of the present universe. It may even be that this type of oscillating vacuum energy density constitutes a significant part of the so-called cold dark matter in the standard Friedmann-Robertson-Walker framework.
Fire, flow and dynamic equilibrium in stream macroinvertebrate communities
Arkle, R.S.; Pilliod, D.S.; Strickler, K.
2010-01-01
The complex effects of disturbances on ecological communities can be further complicated by subsequent perturbations within an ecosystem. We investigated how wildfire interacts with annual variations in peak streamflow to affect the stability of stream macroinvertebrate communities in a central Idaho wilderness, USA. We conducted a 4-year retrospective analysis of unburned (n = 7) and burned (n = 6) catchments, using changes in reflectance values (??NBR) from satellite imagery to quantify the percentage of each catchment's riparian and upland vegetation that burned at high and low severity. For this wildland fire complex, increasing riparian burn severity and extent were associated with greater year-to-year variation, rather than a perennial increase, in sediment loads, organic debris, large woody debris (LWD) and undercut bank structure. Temporal changes in these variables were correlated with yearly peak flow in burned catchments but not in unburned reference catchments, indicating that an interaction between fire and flow can result in decreased habitat stability in burned catchments. Streams in more severely burned catchments exhibited increasingly dynamic macroinvertebrate communities and did not show increased similarity to reference streams over time. Annual variability in macroinvertebrates was attributed, predominantly, to the changing influence of sediment, LWD, riparian cover and organic debris, as quantities of these habitat components fluctuated annually depending on burn severity and annual peak streamflows. These analyses suggest that interactions among fire, flow and stream habitat may increase inter-annual habitat variability and macroinvertebrate community dynamics for a duration approaching the length of the historic fire return interval of the study area. ?? 2009 Blackwell Publishing Ltd.
NASA Astrophysics Data System (ADS)
Yamakoshi, Tomotake; Watanabe, Shinichi; Zhang, Chen; Greene, Chris H.
2013-05-01
The ultracold molecular conversion rate occurring in an adiabatic ramp through a Fano-Feshbach resonance is studied and compared in two statistical models. One model, the so-called stochastic phase-space sampling (SPSS) [Hodby , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.94.120402 94, 120402 (2005)] evaluates the overlap of two atomic distributions in phase space by sampling atomic pairs according to a phase-space criterion. The other model, the chemical equilibrium theory (ChET) [Watabe and Nikuni, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.77.013616 77, 013616 (2008)] considers atomic and molecular distributions in the limit of the chemical and thermal equilibrium. The present study applies SPSS and ChET to a prototypical system of K+K→ K2 in all the symmetry combinations, namely Fermi-Fermi, Bose-Bose, and Bose-Fermi cases. To examine implications of the phase-space criterion for SPSS, the behavior of molecular conversion is analyzed using four distinct geometrical constraints. Our comparison of the results of SPSS with those of ChET shows that while they appear similar in most situations, the two models give rise to rather dissimilar behaviors when the presence of a Bose-Einstein condensate strongly affects the molecule formation.
Effects of electronic correlations and magnetic field on a molecular ring out of equilibrium
NASA Astrophysics Data System (ADS)
Nuss, Martin; von der Linden, Wolfgang; Arrigoni, Enrico
2014-04-01
We study the effects of electron-electron interactions on the steady-state characteristics of a hexagonal molecular ring in a magnetic field as a model for a benzene molecular junction. The system is driven out of equilibrium by applying a bias voltage across two metallic leads. We employ a model Hamiltonian approach to evaluate the effects of on-site as well as nearest-neighbor density-density-type interactions in a physically relevant parameter regime. Results for the steady-state current, charge density, and magnetization in three different junction setups (para, meta, and ortho) are presented. Our findings indicate that interactions beyond the mean-field level renormalize voltage thresholds as well as current plateaus. Electron-electron interactions lead to substantial charge redistribution as compared to the mean-field results. We identify a strong response of the circular current on the electronic structure of the metallic leads. Our results are obtained by steady-state cluster perturbation theory, a systematically improvable approximation to study interacting molecular junctions out of equilibrium, even in magnetic fields. Within this framework, general expressions for the current, charge density, and magnetization in the steady state are derived. The method is flexible and fast and can straightforwardly be applied to effective models as obtained from ab initio calculations.
Molecular dynamic study of pressure fluctuations spectrum in plasma
NASA Astrophysics Data System (ADS)
Bystryi, R. G.
2015-11-01
Pressure of plasma is calculated by using classical molecular dynamics method. The formula based on virial theorem was used. Spectrum pressure's fluctuations of singly ionized non-ideal plasma are studied. 1/f-like spectrum behavior is observed. In other words, flicker noise is observed in fluctuations of pressure equilibrium non-ideal plasma. Relations between the obtained result and pressure fluctuations within the Gibbs and Einstein approaches are discussed. Special attention is paid to features of calculating the pressure in strongly coupled systems.
Novel procedure for thermal equilibration in molecular dynamics simulation.
Gallo, Marco T; Grant, Barry J; Teodoro, Miguel L; Melton, Julia; Cieplak, Piotr; Phillips, George N; Stec, Boguslaw
2009-04-01
We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797
Novel procedure for thermal equilibration in molecular dynamics simulation
Gallo, Marco T.; Grant, Barry J.; Teodoro, Miguel L.; Melton, Julia; Cieplak, Piotr; Phillips, George N.; Stec, Boguslaw
2014-01-01
We describe a simple novel procedure for achieving thermal equilibration between a protein and a surrounding solvent during molecular dynamics (MD) simulation. The method uniquely defines the length of simulation time required to achieve thermal equilibrium over a broad range of parameters, thus removing ambiguities associated with the traditional heuristic approaches. The proposed protocol saves simulation time and avoids bias introduced by the inclusion of non-equilibrium events. The key element of the procedure involves coupling only the solvent atoms to a standard heat bath. Measuring progress towards thermal equilibration involves simply monitoring the difference in temperature between the solvent and the protein. Here, we report that the results of MD simulations using the above procedure are measurably improved relative to the traditional approaches in terms of root-mean-square deviations and principal components analysis both indicating significantly less undesirable divergence. PMID:25125797
Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.
2015-05-21
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.
Schuck, Peter; Gillis, Richard B.; Besong, Tabot M.D.; Almutairi, Fahad; Adams, Gary G.; Rowe, Arthur J.; Harding, Stephen E.
2014-01-01
Sedimentation equilibrium (analytical ultracentrifugation) is one of the most inherently suitable methods for the determination of average molecular weights and molecular weight distributions of polymers, because of its absolute basis (no conformation assumptions) and inherent fractionation ability (without the need for columns or membranes and associated assumptions over inertness). With modern instrumentation it is also possible to run up to 21 samples simultaneously in a single run. Its application has been severely hampered because of difficulties in terms of baseline determination (incorporating estimation of the concentration at the air/solution meniscus) and complexity of the analysis procedures. We describe a new method for baseline determination based on a smart-smoothing principle and built into the highly popular platform SEDFIT for the analysis of the sedimentation behavior of natural and synthetic polymer materials. The SEDFIT-MSTAR procedure – which takes only a few minutes to perform - is tested with four synthetic data sets (including a significantly non-ideal system) a naturally occurring protein (human IgG1) and two naturally occurring carbohydrate polymers (pullulan and λ–carrageenan) in terms of (i) weight average molecular weight for the whole distribution of species in the sample (ii) the variation in “point” average molecular weight with local concentration in the ultracentrifuge cell and (iii) molecular weight distribution. PMID:24244936
NASA Technical Reports Server (NTRS)
Tiwari, S. N.; Jha, M. K.
1993-01-01
Basic formulations, analyses, and numerical procedures are presented to investigate radiative heat interactions in diatomic and polyatomic gases under local and nonlocal thermodynamic equilibrium conditions. Essential governing equations are presented for both gray and nongray gases. Information is provided on absorption models, relaxation times, and transfer equations. Radiative flux equations are developed which are applicable under local and nonlocal thermodynamic equilibrium conditions. The problem is solved for fully developed laminar incompressible flows between two parallel plates under the boundary condition of a uniform surface heat flux. For specific applications, three diatomic and three polyatomic gases are considered. The results are obtained numerically by employing the method of variation of parameters. The results are compared under local and nonlocal thermodynamic equilibrium conditions at different temperature and pressure conditions. Both gray and nongray studies are conducted extensively for all molecular gases considered. The particular gases selected for this investigation are CO, NO, OH, CO2, H2O, and CH4. The temperature and pressure range considered are 300-2000 K and 0.1-10 atmosphere, respectively. In general, results demonstrate that the gray gas approximation overestimates the effect of radiative interaction for all conditions. The conditions of NLTE, however, result in underestimation of radiative interactions. The method developed for this study can be extended to solve complex problems of radiative heat transfer involving nonequilibrium phenomena.
ERIC Educational Resources Information Center
Cloonan, Carrie A.; Andrew, Julie A.; Nichol, Carolyn A.; Hutchinson, John S.
2011-01-01
This article describes an activity that can be used as an inquiry-based laboratory or demonstration for either high school or undergraduate chemistry students to provide a basis for understanding both vapor pressure and the concept of dynamic phase equilibrium. The activity includes a simple setup to create a closed system of only water liquid and…
Molecular dynamics studies of interfacial water at the alumina surface.
Argyris, Dr. Dimitrios; Ho, Thomas; Cole, David
2011-01-01
Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.
Modeling the Hydrogen Bond within Molecular Dynamics
ERIC Educational Resources Information Center
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
ERIC Educational Resources Information Center
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.
Molecular ions, Rydberg spectroscopy and dynamics
Jungen, Ch.
2015-01-22
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.
Parallel Molecular Dynamics Program for Molecules
Energy Science and Technology Software Center (ESTSC)
1995-03-07
ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.
Calculation of transport properties of liquid metals and their alloys via molecular dynamics
NASA Astrophysics Data System (ADS)
Cherne, Frank Joseph, III
The advanced casting modeler requires accurate viscosity and diffusivity data of liquid metals and their alloys. The present work discusses the use of equilibrium and non-equilibrium molecular dynamics techniques to obtain such data without having to rely on oversimplified phenomenological expressions or difficult and expensive experiments. Utilizing the embedded atom method (EAM), the viscosities and diffusivities for a series of equilibrium and non-equilibrium molecular dynamics simulations of nickel, aluminum, and nickel-aluminum alloys are presented. A critical comparison between the equilibrium and non-equilibrium methods is presented. Besides the transport properties, structural data for the liquids are also evaluated. EAM does a poor job of describing the transport properties of nickel-aluminum alloys, particularly near the equiatomic concentration. It has been suggested that charge transfer between nickel and aluminum atoms is responsible for the discrepancy between numerical calculations and available experimental data. A modified electronic distribution function has been developed to simulate the charge transfer associated with compound formation. The effects of such a "charge transfer" modification to the embedded atom method are evaluated. The results of these simulations indicate that the embedded atom method combined with molecular dynamics may be used as a method to predict reasonably the transport properties.
Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity
O'Meara, Brian C.; Smith, Stacey D.; Armbruster, W. Scott; Harder, Lawrence D.; Hardy, Christopher R.; Hileman, Lena C.; Hufford, Larry; Litt, Amy; Magallón, Susana; Smith, Stephen A.; Stevens, Peter F.; Fenster, Charles B.; Diggle, Pamela K.
2016-01-01
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years. PMID:27147092
Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity.
O'Meara, Brian C; Smith, Stacey D; Armbruster, W Scott; Harder, Lawrence D; Hardy, Christopher R; Hileman, Lena C; Hufford, Larry; Litt, Amy; Magallón, Susana; Smith, Stephen A; Stevens, Peter F; Fenster, Charles B; Diggle, Pamela K
2016-05-11
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years. PMID:27147092
Fermionic Molecular Dynamics for Nuclear Dynamics and Thermodynamics
NASA Astrophysics Data System (ADS)
Hasnaoui, K. H. O.; Chomaz, Ph; Gulminelli, F.
A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented.
Rabosky, Daniel L
2012-08-01
The hypothesis of punctuated equilibrium proposes that most phenotypic evolution occurs in rapid bursts associated with speciation events. Several methods have been developed that can infer punctuated equilibrium from molecular phylogenies in the absence of paleontological data. These methods essentially test whether the variance in phenotypes among extant species is better explained by evolutionary time since common ancestry or by the number of estimated speciation events separating taxa. However, apparent "punctuational" trait change can be recovered on molecular phylogenies if the rate of phenotypic evolution is correlated with the rate of speciation. Strong support for punctuational models can arise even if the underlying mode of trait evolution is strictly gradual, so long as rates of speciation and trait evolution covary across the branches of phylogenetic trees, and provided that lineages vary in their rate of speciation. Species selection for accelerated rates of ecological or phenotypic divergence can potentially lead to the perception that most trait divergence occurs in association with speciation events. PMID:22834758
NASA Astrophysics Data System (ADS)
Tovbin, Yu. K.
2015-09-01
Consequences of the complete system of transfer equations of the properties (momentum, energy, and mass) of particles and their pairs are considered under local equilibrium conditions with regard to the Bogoliubov hierarchy of relaxation times between the first and second distribution functions (DFs) and distinctions in the characteristic relaxation times of particle momentum, energy, and mass. It is found that even under the local equilibrium condition in the Bogoliubov hierarchy of relaxation times between the first and second DFs, pair correlations are maintained between all dynamic variables (velocity, temperature, and density) whose values are proportional to the gradients of transferable properties. A criterion is introduced requiring there be no local equilibrium condition upon reaching the critical value at which the description of the transfer process becomes incorrect in classical nonequilibrium thermodynamics. External forces are considered in the equations for strongly nonequilibrium processes. Along with allowing for intermolecular potentials, it becomes possible to discuss the concept of passive forces (introduced in thermodynamics by Gibbs) from the standpoint of the kinetic theory. It is shown that use of this concept does not reflect modern representations of real processes.
Molecular dynamics: A stitch in time
NASA Astrophysics Data System (ADS)
Deupi, Xavier
2014-01-01
Lengthy molecular dynamics simulations of complex systems at the atomic scale usually require supercomputers. Now, by stitching together many shorter independent simulations run 'in the cloud', this requirement has been circumvented, allowing two milliseconds of the dynamics of a G-protein-coupled receptor to be simulated.
Floodplain persistence and dynamic-equilibrium conditions in a canyon environment
NASA Astrophysics Data System (ADS)
Tranmer, Andrew W.; Tonina, Daniele; Benjankar, Rohan; Tiedemann, Matthew; Goodwin, Peter
2015-12-01
Canyon river systems are laterally constrained by steep walls, strath terraces, and bedrock intrusions; however, semialluvial reaches are nested within these environments as discontinuous floodplains along the river margins. These semialluvial floodplains provide an example of dynamic-equilibrium set within high-energy fluvial systems, marking areas where the river is free to alter its boundary conditions. Most research has focused on hydraulic conditions necessary for floodplain formation and persistence in unconfined systems, whereas little is known about canyon streams. This paper focuses on (1) characterizing dynamic-equilibrium, (2) describing the controls on floodplain formation and distribution, and (3) evaluating the performance of extremal hypotheses to identify dynamic-equilibrium and floodplain persistence in high-energy, semiconfined canyon environments. These objectives were addressed with field and numerical data derived from a one-dimensional hydraulic model for bankfull and 100-year return interval flood events, supported by closely spaced cross sections for the lower 38-km canyon reach of the Deadwood River (Idaho). Under bankfull conditions, critical energy thresholds for equilibrium floodplain persistence at this study site present the upper limits of: slope = 0.018, shear stress = 175 N/m2, and specific stream power = 400 W/m2. Channel and floodplains near equilibrium, quantified with a near-zero sediment transport divergence (Exner equation), were successfully identified by the minimum unit stream power extremal hypothesis and to a lesser degree by the other extremal hypotheses that minimize energy expenditure (minimum specific stream power, minimum total stream power, and minimum Froude number), provided backwater environments and major tributaries could be identified. Extremal results were compared to hydraulic geometry relations to evaluate how closely equilibrium floodplains approached values for unconfined alluvial river systems.
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. PMID:27325090
Molecular dynamics simulations: advances and applications
Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L
2015-01-01
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
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. PMID:26949976
Molecular dynamics simulations of large macromolecular complexes
Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus
2015-01-01
Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770
Bjorgaard, J A; Velizhanin, K A; Tretiak, S
2016-04-21
The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited statemolecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited statemolecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission. PMID:27389206
Collective Flocking Dynamics: Long Rang Order in a Non-Equilibrium 2D XY Model
NASA Astrophysics Data System (ADS)
Tu, Yuhai
1996-03-01
We propose and study a non-equilibrium continuum dynamical model for the collective motion of large groups of biological organisms (e.g., flocks of birds, slime molds, schools of fishs, etc.) (J. Toner and Y. Tu, Phys. Rev. Lett.), 75(23), 4326(1995) Our model becomes highly non-trivial, and different from the equilibrium model, for d
Exploiting molecular dynamics in Nested Sampling simulations of small peptides
NASA Astrophysics Data System (ADS)
Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor
2016-04-01
Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.
Star formation and molecular hydrogen in dwarf galaxies: a non-equilibrium view
NASA Astrophysics Data System (ADS)
Hu, Chia-Yu; Naab, Thorsten; Walch, Stefanie; Glover, Simon C. O.; Clark, Paul C.
2016-06-01
We study the connection of star formation to atomic (H I) and molecular hydrogen (H2) in isolated, low-metallicity dwarf galaxies with high-resolution (mgas = 4 M⊙, Nngb = 100) smoothed particle hydrodynamics simulations. The model includes self-gravity, non-equilibrium cooling, shielding from a uniform and constant interstellar radiation field, the chemistry of H2 formation, H2-independent star formation, supernova feedback and metal enrichment. We find that the H2 mass fraction is sensitive to the adopted dust-to-gas ratio and the strength of the interstellar radiation field, while the star formation rate is not. Star formation is regulated by stellar feedback, keeping the gas out of thermal equilibrium for densities n < 1 cm-3. Because of the long chemical time-scales, the H2 mass remains out of chemical equilibrium throughout the simulation. Star formation is well correlated with cold (T ≤ 100 K) gas, but this dense and cold gas - the reservoir for star formation - is dominated by H I, not H2. In addition, a significant fraction of H2 resides in a diffuse, warm phase, which is not star-forming. The interstellar medium is dominated by warm gas (100 K < T ≤ 3 × 104 K) both in mass and in volume. The scaleheight of the gaseous disc increases with radius while the cold gas is always confined to a thin layer in the mid-plane. The cold gas fraction is regulated by feedback at small radii and by the assumed radiation field at large radii. The decreasing cold gas fractions result in a rapid increase in depletion time (up to 100 Gyr) for total gas surface densities Σ _{H I+H_2} ≲ 10 M⊙ pc-2, in agreement with observations of dwarf galaxies in the Kennicutt-Schmidt plane.
Micellar crystals in solution from molecular dynamics simulations
Anderson, J.; Lorenz, C.; Travesset, A.
2008-05-14
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers.
High temperature phonon dispersion in graphene using classical molecular dynamics
Anees, P. Panigrahi, B. K.; Valsakumar, M. C.
2014-04-24
Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the Γ point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 K the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to Γ along K-Γ direction, which indicates instability of the flat 2D graphene sheets.
Is the microscopic stress computed from molecular simulations in mechanical equilibrium?
NASA Astrophysics Data System (ADS)
Torres-Sánchez, Alejandro; Vanegas, Juan M.; Arroyo, Marino
The microscopic stress field connects atomistic simulations with the mechanics of materials at the nano-scale through statistical mechanics. However, its definition remains ambiguous. In a recent work we showed that this is not only a theoretical problem, but rather that it greatly affects local stress calculations from molecular simulations. We find that popular definitions of the local stress, which are continuously being employed to understand the mechanics of various systems at the nanoscale, violate the continuum statements of mechanical equilibrium. We exemplify these facts in local stress calculations of defective graphene, lipid bilayers, and fibrous proteins. Furthermore, we propose a new physical and sound definition of the microscopic stress that satisfies the continuum equations of balance, irrespective of the many-body nature of the inter-atomic potential. Thus, our proposal provides an unambiguous link between discrete-particle models and continuum mechanics at the nanoscale.
Influence of non-equilibrium carrier dynamics on pulse amplification in semiconductor gain media
NASA Astrophysics Data System (ADS)
Böttge, C. N.; Hader, J.; Kilen, I.; Koch, S. W.; Moloney, J. V.
2015-03-01
The influence of non-equilibrium carrier dynamics on pulse propagation through inverted semiconductor gain media is investigated. For this purpose, a fully microscopic many-body model is coupled to a Maxwell solver, allowing for a self-consistent investigation of the light-matter-coupling and carrier dynamics, the optical response of the laser and absorber in the multiple-quantum-well medium, and the modification of the light field through the resulting optical polarization. The influence of the intra-pulse dynamics on the magnitude and spectral dependence of pulse amplification for single pulses passing through inverted quantum-well media is identified. In this connection, the pulse-induced non-equilibrium deviations of the carrier distributions, the kinetic-hole filling kinetics in the gain medium, and the saturable-absorber-relaxation dynamics are scrutinized. While pulses shorter than about 100 fs are found to be rather unaffected by the carrier-relaxation dynamics, the pump-related dynamics become prominent for pulses in the multi-picosecond range leading to significant amplification.