Constrained reaction coordinate dynamics for systems with constraints

In the context of molecular dynamics simulations of rare events, the application of constraints on a suitable reaction coordinate has often been found useful for sampling of the free energy barrier. The efficiency of these calculations is hampered by geometrical difficulties, related to the metric factor and inertial forces. Some years ago Mulders et al. [1996, J. chem. Phys., 104, 48691 suggested a way to simplify the approach. Their idea was demonstrated shortly afterwards by Sprik and Ciccotti [1998, J. chem. Phys., 109, 77371. The present paper extends these results to vector reaction coordinate and molecular systems modelled with holonomic constraints.     

Free energy from molecular dynamics with multiple constraints

In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to constrain the reaction coordinate to a constant value, but the metric tensor effect of the constraint on the sampled phase space distribution complicates this relation. The appropriately corrected expression for the potential of mean constraint force method (PMCF) for systems in which only the reaction coordinate is constrained was published recently. Here we will consider the general case of a system with multiple constraints. This situation arises when both the reaction coordinate and the ‘hard’ coordinates are constrained, and also in systems with several reaction coordinates. The obvious advantage of this method over the established thermodynamic integration and free energy perturbation methods is that it avoids the cumbersome introduction of a full set of generalized coordinates complementing the constrained coordinates. Simulations of n-butane and n-pentane in vacuum illustrate the method.     

Interfacial reaction rates and free energy of cubic clusters

A new formulation of interfacial reaction rates for clusters in binary alloys is presented. It accounts for the matrix structure and the topological properties of the clusters at the atomic scale. It is shown that the probabilities per unit time that a solute atom be captured or released by a cluster are functions not only of the partition function but also of a transition function. The principles of calculation of these functions are general but only the case of cubic clusters is treated here (results can be used for L₁₂ clusters in fcc matrices). Exact calculations have been done for small clusters (size<10), followed by a Monte-Carlo sampling method for intermediate sizes as a function of temperature and interaction energy (a material characteristic). Finally, it is shown that generic results can be extrapolated at higher cluster size in a large range of temperature and/or interaction energy.     

The free energy of lattice gauge theories at large β

An upper and a lower bound for the free energy density of a lattice gauge teory with compact gauge group are derived, valid for all values of β. For large β the first two terms of the asymptotic expansions of these bounds coincide, thus determining the corresponding terms of the free energy density. Moreover the gauge groups U(N) and SU(N) are treated explicitly.     

Lagrangian formulation of a general Hamiltonian theory with constraints

A Lagrangian formulation is constructed for a general Hamiltonian theory with constraints. A modification is proposed of the standard procedure of the Hamiltonianization of a Lagrangian theory in the case when the Lagrangian theory has primary constraints. The obtained results are used to establish the Lagrangian form of infinitesimally small canonical transformations in the Hamiltonian formalism.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 3, pp. 104–112, March, 1986.     

Quantum mechanical free energy barrier for an enzymatic reaction

We discuss problems related to in silico studies of enzymes and show that accurate and converged free energy changes for complex chemical reactions can be computed if a method based on a thermodynamic cycle is employed. The method combines the sampling speed of molecular mechanics with the accuracy of a high-level quantum mechanics method. We use the method to compute the free energy barrier for a methyl transfer reaction catalyzed by the enzyme catechol O-methyltransferase at the level of density functional theory. The surrounding protein and solvent are found to have a profound effect on the reaction, and we show that energies can be extrapolated easily from one basis set and exchange-correlation functional to another. Using this procedure we calculate a barrier of 69 kJ/mol, in excellent agreement with the experimental value of 75 kJ/mol.     

The free energy of a class of Hopfield models

We show that in the limitp ,N 0,=p/N 0 the limit free energy of the Hopfield model equals in probability the Curie-Weiss free energy. We prove also that the free energy of the Hopfield model is self-averaging for any finite .     

Surface free energy of a finite system without interfaces at low temperatures

We derive the specific surface free energy for a rather general system at low temperatures that can be rewritten as a gas of non-interacting contours (polymers). To this end, we use a standard cluster expansion series for the system?s partition function. A specific regime of ‘weak’ boundary conditions is assumed to ensure that no interfaces or large droplets occur in the system. We illustrate the general results, using a simple lattice–gas model.     

Lorentz violation at high energy: Concepts, phenomena, and astrophysical constraints

We consider here the possibility of quantum gravity induced violation of Lorentz symmetry (LV). Even if suppressed by the inverse Planck mass such LV can be tested by current experiments and astrophysical observations. We review the effective field theory approach to describing LV, the issue of naturalness, and many phenomena characteristic of LV. We discuss some of the current observational bounds on LV, focusing mostly on those from high energy astrophysics in the QED sector at order E/M_Planck. In this context, we present a number of new results which include the explicit computation of rates of the most relevant LV processes, the derivation of a new photon decay constraint, and modification of previous constraints taking proper account of the helicity dependence of the LV parameters implied by effective field theory.     

色散作用能更简捷的推导

基于色散作用的本质，利用宏观电介质形式，更一般且更简捷地得到了各种维度的色散作用能。     

Breaking free of electrical constraints

Photonic interconnections provide a viable means to overcome the fundamental limitations imposed upon computer system topologies by electrical signaling. Direct board-to-board (or assembly-to-assembly) signaling, without need of a backplane, provides multiple points of connectivity between adjacent electronic complexes while obviating the need to route all board-level signals to and through a central connector choke point. Optical busses can permit full-speed signaling between multiple chips, memory units, or processing units without requiring an active control plane. One-to-many and all-to-all photonic broadcasts greatly simplify multi-processor and multi-core system design.     

Dynamical switching of a reaction coordinate to carry the system through to a different product state at high energies

Questions of how the nature of a reaction coordinate that dominates the reaction ceases to exist and whether some new features emerge as an increase of total energy of systems are investigated for many degrees of freedom Hamiltonian systems. As a model system, a hydrogen atom in crossed electric and magnetic fields is scrutinized. It is shown that, when the total energy increases, the reaction coordinate no longer dominates the reaction as did at the lower energies. In turn, a new reaction coordinate emerges, connecting totally different reactant and product states. Furthermore, depending on which parts of the phase space the system traverses through the saddle, the system nonuniformly experiences the switching of the reaction coordinate leading to the different product state. The universal mechanism of the cessation and the switching of the reaction coordinate at high energy regimes above the saddle is investigated.     

Einstein-Podolsky-Rosen constraints on quantum action at a distance: The Sutherland paradox

Assuming that future experiments confirm Aspect's discovery of nonlocal interactions between quantum pairs of correlated particles, we analyze the constraints imposed by the EPR reasoning on the said interactions. It is then shown that the nonlocal relativistic quantum potential approach plainly satisfies the Einstein causality criteria as well as the energy-momentum conservation in individual microprocesses. Furthermore, this approach bypasses a new causal paradox for timelike separated EPR measurements deduced by Sutherland in the frame of an approach by means of space-time zigzags with advanced potentials. It is finally demonstrated that this inherent quantum causal direct interaction establishes permanent EPR correlations which are always restricted to spacelike separations and are instantaneous only in the center-of-mass rest frame of the two-particle system.     

The free energy of the spin-boson model

Forn spins 1/2 coupled linearly to a boson field in a volumeV _n, the existence of the specific free energy is proved in the limitn ,V _n withn/V _n=const. The interaction is essentially of the mean field type, in as much as it is proportional to 1/V _n; the coupling constants are allowed to be spin dependent. A variational expression is obtained for the limiting specific free energy, and a critical temperature is identified above which the system behaves as if there were no coupling at all.     

Canonical formulation of the theory of a free integral-spin massive field

A Lagrangian is constructed for free integral-spin massive fields in space — time of arbitrary dimension. The Hamiltonian of the theory is found and the structure and algebra of the couplings are established.Tomsk State University. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 2, pp. 100–105, February, 1995.     

Surface free energy of platinum nanoparticles at zero pressure: A molecular dynamic study

Metallic nanoparticles are interesting because of their use in catalysis and sensors. The surface energy of the FCC platinum nanoparticles are investigated via molecular dynamics simulation using Quantum Sutton–Chen (QSC) potential. We have calculated the Gibbs free energy for the FCC platinum bulk and also for its nanoparticle. All calculations have been carried out at zero pressure. We have used the thermodynamic integration method to obtain the Gibbs free energy. The total Gibbs free energy is taken as the sum of its central bulk and its surface free energy. We have calculated the free energy of a platinum nanoparticle as a function of temperature.     

Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments

To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive dynamics. Here, we invoke the splitting probability as a test of the suitability of such a proposed reaction coordinate. Comparison of the observed splitting probability with that computed from the kinetic model provides a simple test to reject poor reaction coordinates. We demonstrate this test for a force spectroscopy measurement of a DNA hairpin.