Use of the Rotation Vector in Brownian Dynamics Simulation of Transient Electro‐Optical Properties

We have recently developed a new singularity‐free algorithm for Brownian dynamics simulation of free rotational diffusion. The algorithm is rigorously derived from kinetic theory and makes use of the Cartesian components of the rotation vector as the generalized coordinates describing angular orientation. Here, we report on the application of this new algorithm in Brownian dynamics simulations of transient electro‐optical properties. This work serves two main purposes. Firstly, it demonstrates the integrity of the new algorithm for BD‐simulations of the most common transient electro‐optic experiments. Secondly, it provides new insight into the performance of the new algorithm compared to algorithms that make use of the Euler angles. We study the transient electrically induced birefringence in dilute solutions of rigid particles with anisotropic polarization tensor in response to external electric field pulses. The use of both one single electric pulse and two electric pulses with opposite polarity are being analyzed. We document that the new singularity‐free algorithm performs flawlessly. We find that, for these types of systems, the new singularity‐free algorithm, in general, outperforms similar algorithms based on the Euler angles. In a wider perspective, the most important aspect of this work is that it serves as an important reference for future development of efficient BD‐algorithms for studies of more complex systems. These systems include polymers consisting of rigid segments with single‐segment translational–rotational coupling, segment–segment fluid‐dynamic interactions and holonomic constraints.

     

Singularity‐Free Brownian Dynamics Analyses of Rotational Dynamics: Non‐Spherical Nanoparticles in Solution

Summary: From kinetic theory we have rigorously derived singularity‐free Brownian dynamics analyses of nanoparticle rotational dynamics. The rigid non‐spherical nanoparticles incorporate all three rotational degrees of freedom. This was achieved by using the components of Cartesian rotation vectors as the generalized coordinates describing angular orientation. The new results constitute an important advance compared to the situation when Eulerian angles specify angular orientation. Our finding eliminates one of the main longstanding obstacles to detailed studies of nanoparticle rotational dynamics in the diffusion time domain. The described formalism is applicable to a wide range of nanoparticle systems including liquid crystals, biopolymers, and colloids.

     

Transient molecular electro-optics Cartesian rotation vector versus Eulerian angles

Comparing the Euler angles, the classical choice of generalized coordinates describing the three rotational degrees of freedom of a rigid body, and the Cartesian rotation vector, we show that they both have their advantages and disadvantages in kinetic theory and Brownian dynamics analysis of molecular electro-optics. The Eulerian angles often yield relatively simple, yet singular, equations of motion, while their counterparts expressed in terms of Cartesian rotation vector are non-singular but more complex. In a special case, we show that the generalized force associated with the Cartesian rotation vector equals the torque. In addition, we introduce a new graphical approach to qualitatively track how changes in the Eulerian angles affect the Cartesian rotation vector.     

Hierarchy of equations in the generalized density functional theory

Functional relations and equations of hierarchy in the generalized density functional theory (DFT) are derived from coordinate scaling and adiabatic connection. Local and nonlocal solutions for the noninteracting kinetic energy, exchange energy, correlation energy, and the kinetic energy correction functionals are presented. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Polypeptide folding on a conformational‐space network: Dependence of network topology on the structural discretization procedure

Mapping the conformational space of a polypeptide onto a network of conformational states involves a number of subjective choices, mostly in relation to the definition of conformation and its discrete nature in a network framework. Here, we evaluate the robustness of the topology of conformational‐space networks derived from Molecular Dynamics (MD) simulations with respect to the use of different discretization (clustering) methods, variation of their parameters, simulation length and analysis time‐step, and removing high‐frequency motions from the coordinate trajectories. In addition, we investigate the extent to which polypeptide dynamics can be reproduced on the resulting networks when assuming Markovian behavior. The analysis is based on eight 500 ns and eight 400 ns MD simulations in explicit water of two 10‐residue peptides. Three clustering algorithms were used, two of them based on the pair‐wise root‐mean‐square difference between structures and one on dihedral‐angle patterns. A short characteristic path length and a power‐law behavior of the probability distribution of the node degree are obtained irrespective of the clustering method or the value of any of the tested parameters. The average cliquishness is consistently one or two orders of magnitude larger than that of a random realization of a network of corresponding size and connectivity. The cliquishness as function of node degree and the kinetic properties of the networks are found to be most dependent on clustering method and/or parameters. Although Markovian simulations on the networks reproduce cluster populations accurately, their kinetic properties most often differ from those observed in the MD simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Coordinate measurements and operators

Relativistic quantum-field theory provides the machinery for calculating wave functions or probability amplitudes depending upon space-time coordinates. The currently accepted theory, however, fails to provide position operators and a means of measuring particle coordinates that are consistent with Dirac's properties of physical observables. This is because it calls for a space position probability distribution at a specified time. This paper shows, however, that space-time event coordinate operators, together with a corresponding measurement procedure, can be found that are consistent with Dirac's requirements. This is done through a reinterpretation of the amplitudes computed by field theory and does not involve any change in that mathematical formalism. The measurement of the space-time coordinates of an event is accomplished by detecting the absorption of a photon by a particle from each of two light pulses designed to overlap at a given point at a given time. If a final emitted photon has an energy whose sum with the final particle energy approximately equals the sum of the mean energies of the pulses, then the absorption of the two pulse photons must certainly have taken place within a distance the order of a Compton wavelength of the small space-time region of overlapping pulses. This is clear from the fact that the high energy required to confine the pulses to very small volumes must throw a particle absorbing them far off the mass shell. Thus the absorption of the two photons throws the particle into a narrowly confined spatial wave function that must decay extremely rapidly—to within a Compton wavelength, a delta function in space-time. This delta function is the eigenfunction of space-time coordinate operators X^μ and is the scalar product of vectors in a Hilbert space spanned by spin–space-time kets large enough to contain the operators of the Poincaré group. These event operators transform properly under the action of Poincaré operators but do not commute with the mass. If the Compton wavelength is not negligible compared to the accuracy desired in the coordinate measurements, individual coordinate measurements are no longer possible. Nevertheless, a large number of repeated coordinate measurements can be carried out to produce a coordinate probability distribution. This distribution can be unfolded to find a true coordinate probability distribution if the charge form factor is known from basic theory. An analysis of laboratory particle detection techniques shows that they actually determine space coordinates and energy rather than spatial coordinates at a given time. When this fact is included, the Klein–Nishina formula can be derived using the electromagnetic four-vector potential as the photon probability amplitude wave. To clarify the meaning of the observables, a mass-momentum measurement is described.     

Multiple protonation equilibria in electrostatics of protein-protein binding

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.     

Model hysteresis dimer molecule II: deductions from probability profile due to system coordinates

The hysteresis dimer reaction of the first sequel is applied to test the Gibbs density-in-phase hypothesis for a canonical distribution at equilibrium. The probability distribution of variously defined internal and external variables is probed using the algorithms described, in particular the novel probing of the energy states of a labeled particle where it is found that there is compliance with the Gibbs’ hypothesis for the stated equilibrium condition and where the probability data strongly suggests that an extended equipartition principle may be formulated for some specific molecular coordinates, whose equipartition temperature does not equal the mean system temperature and a conjecture concerning which coordinates may be suitable is provided. Evidence of violations to the mesoscopic nonequilibrium thermodynamics (MNET) assumptions used without clear qualifications for a canonical distribution for internal variables are described, and possible reasons outlined, where it is found that the free dimer and atom particle kinetic energy distributions agree fully with Maxwell–Boltzmann statistics but the distribution for the relative kinetic energy of bonded atoms does not. The principle of local equilibrium (PLE) commonly used in nonequilibrium theories to model irreversible systems is investigated through NEMD simulation at extreme conditions of bond formation and breakup at the reservoir ends in the presence of a temperature gradient, where for this study a simple and novel difference equation algorithm to test the divergence theorem for mass conservation is utilized, where mass is found to be conserved from the algorithm in the presence of flux currents, in contradiction to at least one aspect of PLE in the linear domain. It is concluded therefore that this principle can be a good approximation at best, corroborating previous purely theoretical results derived from the generalized Clausius Inequality, which proved that the PLE cannot be an exact principle for nonequilibrium systems.      

Transformed Dirac equation for the hydrogen atom,comparison with previous approaches in momentum space,and the anomalous Zeeman effect in momentum representation

The solution of a unitarily transformed Dirac equation for the hydrogenic electron in zero magnetic field is investigated here. The momentum‐space representation is adopted as a natural recourse. The spinor part of the transformed wavefunction in momentum space can be easily prescribed for a central potential. Hence, for the Coulomb potential, a pair of equations is obtained for the radial components in momentum space. It is shown that starting from these radial equations, one can recover the equations previously derived by Rubinowicz, Lévy, and Lombardi for the problem of the Dirac hydrogen atom in momentum space. This establishes equivalence among different approaches based on the momentum representation, including the current treatment. The recovery of the equations due to Rubinowicz permits the exact eigenvalues to be written down and exact expressions to be derived for the radial components of the transformed wavefunction in momentum space. A new approach is adopted to carry out a reduction to the nonrelativistic regime and the nonrelativistic limit. At first the transformed momentum‐space equation for the hydrogen atom is rewritten in terms of the hyperspherical coordinates. The zeroth‐order solutions of the new equation are recovered in the limit c → ∞ where c is the speed of light. These are manifestly separable into positive‐ and negative‐energy forms. For positive energy, these solutions have nonvanishing upper components that are two‐component spinors. The latter exactly correspond to the single‐component, nonrelativistic, momentum‐space solutions derived by Fock. It is shown that when the upper component is corrected through first order in v²/c² but the separability is still maintained for the transformed wavefunction, one retrieves the Pauli equation in momentum space. It is also shown that for a hydrogen atom placed in a uniform magnetic field, the nonvanishing momentum‐space matrix elements representing the anomalous Zeeman effect have a simple form, namely, the product of a radial integral and an angular integral. These integrals are equal to the well‐known radial and angular integrals in coordinate representation. The matrix elements can be easily evaluated. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Exploring chemical reactivity of complex systems with path‐based coordinates: Role of the distance metric

Path‐based reaction coordinates constitute a valuable tool for free‐energy calculations in complex processes. When a reference path is defined by means of collective variables, a nonconstant distance metric that incorporates the nonorthonormality of these variables should be taken into account. In this work, we show that, accounting for the correct metric tensor, these kind of variables can provide iso‐hypersurfaces that coincide with the iso‐committor surfaces and that activation free energies equal the value that would be obtained if the committor function itself were used as reaction coordinate. The advantages of the incorporation of the variable metric tensor are illustrated with the analysis of the enzymatic reaction catalyzed by isochorismate‐pyruvate lyase. Hybrid QM/MM techniques are used to obtain the free energy profile and to analyze reactive trajectories initiated at the transition state. For this example, the committor histogram is peaked at 0.5 only when a variable metric tensor is incorporated in the definition of the path‐based coordinate. © 2014 Wiley Periodicals, Inc.     

Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators

New symplectic integrators have been developed by combining molecular dynamics integration with the standard theory of molecular vibrations to solve the Hamiltonian equations of motion. The presented integrators analytically resolve the internal high-frequency molecular vibrations by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of an isolated molecule only. The translation and rotation of a molecule are treated as vibrational motions with the vibrational frequency zero. All types of motion are thus described in terms of the normal coordinates. The method's time reversibility requirement was used to determine the equations of motion for internal coordinate system of a molecule. The calculation of long-range forces is performed numerically within the generalized second-order leap-frog scheme, in the same way as in standard second-order symplectic methods. The new methods for integrating classical equations of motion using normal mode analysis allow us to use a long integration step and are applicable to any system of molecules with one equilibrium configuration.     

Nanoparticle dynamics: a multiscale analysis of the Liouville equation

A theory of nanoparticle dynamics based on scaling arguments and the Liouville equation is presented. We start with a delineation of the scales characterizing the behavior of the nanoparticle/host fluid system. Asymptotic expansions, multiple time and space scale techniques, the resulting coarse-grained dynamics of the probability densities of the Fokker-Planck-Chandrasekhar (FPC) type for the nanoparticle(s), and the hydrodynamic models of the host medium are obtained. Collections of nanoparticles are considered so that problems such as viral self-assembly and the transition from a particle suspension to a solid porous matrix can be addressed via a deductive approach that starts with the Liouville equation and a calibrated atomic force field, and yields a generalized FPC equation. Extensions allowing for the investigation of the rotation and deformation of the nanoparticles are considered in the context of the space-warping formalism. Thermodynamic forces and dissipative effects are accounted for. The notion of configuration-dependent drag coefficients and their implications for coagulation and consolidation are shown to be natural consequences of the analysis. All results are obtained via formal asymptotic expansions in mass, size, and other physical and kinetic parameter ratios.     

CAST: A new program package for the accurate characterization of large and flexible molecular systems

The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry‐adapted perturbation theory‐based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)‐accelerated TeraChem program is available. The program is available on request. © 2014 Wiley Periodicals, Inc.