Diffusion and Brownian motion in Lagrangian coordinates

In this paper we consider the convection-diffusion problem of a passive scalar in Lagrangian coordinates, i.e., in a coordinate system fixed on fluid particles. Both the convection-diffusion partial differential equation and the Langevin equation are expressed in Lagrangian coordinates and are shown to be equivalent for uniform, isotropic diffusion. The Lagrangian diffusivity is proportional to the square of the relative change of surface area and is related to the Eulerian diffusivity through the deformation gradient tensor. Associated with the initial value problem, we relate the Eulerian to the Lagrangian effective diffusivities (net spreading), validate the relation for the case of linear flow fields, and infer a relation for general flow fields. Associated with the boundary value problem, if the scalar transport problem possesses a time-independent solution in Lagrangian coordinates and the boundary conditions are prescribed on a material surface/interface, then the net mass transport is proportional to the diffusion coefficient. This can be also shown to be true for large Peclet number and time-periodic flow fields, i.e., closed pathlines. This agrees with results for heat transfer at high Peclet numbers across closed streamlines.     

Exact solutions of lattice polymer models

We consider directed path models of a selection of polymer and vesicle problems. Each model is used to illustrate an important method of solving lattice path enumeration problems. In particular, the Temperley method is used for the polymer collapse problem. The ZL method is used to solve the semi-continuous vesicle model. The Constant Term method is used to solve a set of partial difference equations for the polymer adsorption problem. The Kernel method is used to solve the functional equation that arises in the polymer force problem. Finally, the Transfer Matrix method is used to solve a problem in colloid dispersions. All these methods are combinatorially similar as they all construct equations by considering the action of adding an additional column to the set of objects.     

Exact quantum mechanical vibration-rotation kinetic energy operator of four-particle system in various coordinates

The vibration-rotational kinetic energy operators of four-particle system in various coordinates are derived using a new and simple angular momentum method. The operators are respectively suitable for studying the systems described by scattering coordinate, valence coordinate, Radau coordinate, Radau/Jacobi and Jacobi/valence hybrid coordinates and so on. Certain properties of these operators and their possible applications are discussed.     

Exact analytical loop closure in proteins using polynomial equations

Loop closure in proteins has been studied actively for over 25 years. Using spherical geometry and polynomial equations, several loop-closure problems in proteins are solved exactly by reducing them to the determination of the real roots of a polynomial. Loops of seven, eight, and nine atoms are treated explicitly, including the tripeptide and disulfide-bonded loop-closure problems. The number of valid loop closures can be evaluated by the method of Sturm chains, which counts the number of real roots of a polynomial. Longer loops can be treated by three methods: by sampling enough dihedral angles to reduce the problem to a soluble loop-closure problem; by applying the loop-closure algorithm hierarchically; or by decimating the chain into independently moving rigid elements that can be reconnected using loop-closure algorithms. Applications of the methods to docking, homology modeling and NMR problems are discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 819–844, 1999     

Exact solutions for interacting finite potential wells

Exact wave functions and eigenenergy relations are obtained for a biwell potential as a function of interwell displacement and single well parameters. The proliferation of energies is shown explicitly as the wells are brought into close proximity. The model is compared with the opaque division-wall model. These results find important application in laser and nuclear physics.     

On existence of steady-state solutions to the coagulation equations

The general steady-state coagulation equations with sources and sinks are examined. These equations are shown to admit physically unacceptable solutions in some cases, and it is hypothesized that in such a case a gelation or precipitation phenomenon occurs. General conditions on the coagulation and loss coefficients are given that insure the existence of physically realistic solutions. The physically realistic solutions have tails that decay faster than any power of particle size.     

Exact solutions for kinetic models of macromolecular dynamics

Dynamic biological processes such as enzyme catalysis, molecular motor translocation, and protein and nucleic acid conformational dynamics are inherently stochastic processes. However, when such processes are studied on a nonsynchronized ensemble, the inherent fluctuations are lost, and only the average rate of the process can be measured. With the recent development of methods of single-molecule manipulation and detection, it is now possible to follow the progress of an individual molecule, measuring not just the average rate but the fluctuations in this rate as well. These fluctuations can provide a great deal of detail about the underlying kinetic cycle that governs the dynamical behavior of the system. However, extracting this information from experiments requires the ability to calculate the general properties of arbitrarily complex theoretical kinetic schemes. We present here a general technique that determines the exact analytical solution for the mean velocity and for measures of the fluctuations. We adopt a formalism based on the master equation and show how the probability density for the position of a molecular motor at a given time can be solved exactly in Fourier-Laplace space. With this analytic solution, we can then calculate the mean velocity and fluctuation-related parameters, such as the randomness parameter (a dimensionless ratio of the diffusion constant and the velocity) and the dwell time distributions, which fully characterize the fluctuations of the system, both commonly used kinetic parameters in single-molecule measurements. Furthermore, we show that this formalism allows calculation of these parameters for a much wider class of general kinetic models than demonstrated with previous methods.     

Exact solutions of a new Coulomb ring-shaped potential

A new Coulomb ring-shaped potential is proposed, which results from adding a potential proportional to(cos θ/r ² sin² θ)to a Coulomb potential. The Schrödinger equation with this new model potential is separated into angular and radial components. The exactly wavefunctions and the spectrum equation for bound state are presented by the standard approach.     

Exact solutions of an asymmetric double well potential

Journal of Mathematical Chemistry - The analytical solutions of an asymmetric double well potential $$V(x)=a, x^2-b, x^3+c, x^4$$ are found to be a triconfluent Heun function $$H_{T}(alpha ,...     

Exact solutions of the rigid rotor in the electric field

We first present a new constraint condition on the confluent Heun function H_C(α, β, γ, δ, η;z) (β, γ ≥ 0, z ∈ [0, 1]) and then illustrate how to solve the rigid rotor in the electric field. We find its exact solutions unsolved previously through solving the Wronskian determinant. The present results compared with those by the perturbation methods are found to have a big difference for a large parameter a. We also present 2D and 3D probability density distributions by choosing different angular momentum quantum numbers l. We observe that the original eigenvalues with degeneracy (2 l + 1) are split into the (l + 1) state with approximate eigenvalues l(l + 1) for small a but large l.     

Exact and approximate solutions to the one-center McMurchie–Davidson tree-search problem

We have attempted to optimize the cost (the total number of floating-point operations required) of using the McMurchie–Davidson R_NLMj recurrence relation. Rigorous solutions of the tree-search problem inherent in the cost minimization are given for total angular momentum L ≤ 7. For L ≥ 8, the rigorous search algorithm is prohibitively expensive, and we propose an approximate algorithm that generates highly optimized trees. Cost comparisons demonstrate that the present scheme is consistently superior to two others currently in use.     

The rotation–vibration coupling equations for polyatomic molecules in internal coordinates

An exact vibration–rotation kinetic energy operator for polyatomic molecules has been obtained on the basis of Sutcliffe's method, in terms of curvilinear internal coordinates and rotational angular moment operators. This operator is derived from the kinetic energy operator in Cartesian coordinates by the successive transformations using the chain rule. This kinetic energy operator can be used not only for the system of any triatomic and tetraatomic molecules and common polyatomic molecules in chemistry, but also for the investigation of the collision problems between two molecules after some modifications. Finally, using this Hamiltonian, the rotation–vibration coupling equations of polyatomic molecules have been derived and discussed. © 1992 John Wiley & Sons, Inc.     

Exact solutions and coherent states for a generalized potential

Exact solutions of the vibrational Schrödinger equation for a generalized potential energy function \(\hbox {V(R)}=\hbox {C}_{0}(\mathrm{{R}-\mathrm {R}}_{\mathrm{e}})^{2}/[\hbox {aR}\,+\,(\mathrm{{b}-\mathrm {a}})\hbox {R}_{\mathrm{e}}]^{2}\) are obtained. It includes those of Dunham, Ogilvie and Simons–Parr–Finlan potentials as special cases corresponding to b \(=\) 1, a \(=\) 0, 1/2, 1, respectively. The analytical wave functions derived are useful to test the quality of numerical methods or to perform perturbative or variational calculations for the problems that cannot be solved exactly. Coherent states for generalized potential, which minimize the position–momentum uncertainty relation are also constructed.     

Body-fixed equations for atom-molecule scattering: Exact and centrifugal decoupling methods

We demonstrate an exact method for solving the close-coupled equations for rotationally inelastic scattering in the body-fixed (BF) coordinate representation, using a slight modification of the exponential method which allows application of the known boundary conditions for the space-fixed (SF) coordinate frame. The nature of the coupling in the BF frame suggests approximations which reduce the problem to a set of problems each of a smaller dimensionality. Using an atom-rigid rotor model potential, we have compared the decoupling approximation suggested by Pack and by McGuire and Kouri to the fully coupled problem. We find the centrifugal decoupling (CD) approximation to work best at low total angular momenta J, and for low rotor states j. Opacity functions for inelastic transitions are generally better than ones for elastic transitions, due to errors in the phases of elastic S-matrix elements. However, at high J, CD often severely underestimates the inelastic transition probabilities.     

Exact solutions for spherically confined hydrogen‐like atoms

We present exact analytical solutions for the much‐studied problem of a hydrogen‐like atom confined in a spherical box of radius R. These solutions, which are obtained for all states and all R, are expressed directly in terms of the Kummer M‐functions whose analytical and numerical properties are well known, and may be calculated using standard computing packages. The solutions are illustrated by precise calculations that yield accurate energies E for any given radius R, or for R when E is known. In the special case where E = 0, it is shown that the solution may be expressed in terms of Bessel functions. Finally, the physical assumptions made in applying this model to describe atomic confinement are discussed critically. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

An analytical approach to solutions of master equations for stochastic nonlinear reactions

In this paper we consider a class of nonlinear reactions which are important in stochastic reaction networks. We find the exact solution of the chemical master equation for a class of irreversible and reversible nonlinear reactions. We also present the explicit form of the equilibrium probability solution of the reactions. The results can be used for analyzing stochastic dynamics of important reactions such as binding/unbinding reaction and protein dimerization.     

Exact solutions for the entropy production rate of several irreversible processes

We investigate thermal conduction described by Newton's law of cooling and by Fourier's transport equation and chemical reactions based on mass action kinetics where we detail a simple example of a reaction mechanism with one intermediate. In these cases we derive exact expressions for the entropy production rate and its differential. We show that at a stationary state the entropy production rate is an extremum if and only if the stationary state is a state of thermodynamic equilibrium. These results are exact and independent of any expansions of the entropy production rate. In the case of thermal conduction we compare our exact approach with the conventional approach based on the expansion of the entropy production rate near equilibrium. If we expand the entropy production rate in a series and keep terms up to the third order in the deviation variables and then differentiate, we find out that the entropy production rate is not an extremum at a nonequilibrium steady state. If there is a strict proportionality between fluxes and forces, then the entropy production rate is an extremum at the stationary state even if the stationary state is far away from equilibrium.