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In this paper, we describe a new and fully coherent stochastic surface hopping method for simulating mixed quantum-classical systems. We illustrate the approach on the simple but unforgiving problem of quantum evolution of a two-state quantum system in the limit of unperturbed pure state dynamics and for dissipative evolution in the presence of both stationary and nonstationary random environments. We formulate our approach in the Liouville representation and describe the density matrix elements by ensembles of trajectories. Population dynamics are represented by stochastic surface hops for trajectories representing diagonal density matrix elements. These are combined with an unconventional coherent stochastic hopping algorithm for trajectories representing off-diagonal quantum coherences. The latter generalizes the binary (0,1) "probability" of a trajectory to be associated with a given state to allow integers that can be negative or greater than unity in magnitude. Unlike existing surface hopping methods, the dynamics of the ensembles are fully entangled, correctly capturing the coherent and nonlocal structure of quantum mechanics. [ABSTRACT FROM AUTHOR]

Stochastic simulation for in silico studies of large biochemical networks requires a great amount of computational time. We recently proposed a new exact simulation algorithm, called the rejectionbased stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)], to improve simulation performance by postponing and collapsing as much as possible the propensity updates. In this paper, we analyze the performance of this algorithm in detail, and improve it for simulating large-scale biochemical reaction networks. We also present a new algorithm, called simultaneous RSSA (SRSSA), which generates many independent trajectories simultaneously for the analysis of the biochemical behavior. SRSSA improves simulation performance by utilizing a single data structure across simulations to select reaction firings and forming trajectories. The memory requirement for building and storing the data structure is thus independent of the number of trajectories. The updating of the data structure when needed is performed collectively in a single operation across the simulations. The trajectories generated by SRSSA are exact and independent of each other by exploiting the rejection-based mechanism. We test our new improvement on real biological systems with a wide range of reaction networks to demonstrate its applicability and efficiency. [ABSTRACT FROM AUTHOR]

The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterionmediated free energy conclusively directs folding into a compact structure. [ABSTRACT FROM AUTHOR]

In this paper, a previous coarse-grain model [J. T. Padding and W. J. Briels, J. Chem. Phys. 117, 925 (2002)] to simulate melts of linear polymers has been adapted to simulate polymers with more complex hierarchies. Bond crossings between highly coarse-grained soft particles are prevented by applying an entanglement algorithm. We first test our method on a virtual branch point inside a linear chain to make sure it works effectively when linking two linear arms. Next, we apply our method to study the diffusive and rheological behaviors of a melt of three-armed stars. We find that the diffusive behavior of the three-armed star is very close to that of a linear polymer with the same molecular weight, while its rheological properties are close to those of a linear chain with molecular mass equal to that of the longest linear sub-chain in the star. [ABSTRACT FROM AUTHOR]

In this paper, we present time-reversible simulation algorithms for rigid bodies in the quaternion representation. By advancing a time-reversible algorithm [Y. Kajima, M. Hiyama, S. Ogata, and T. Tamura, J. Phys. Soc. Jpn. 80, 114002 (2011)] that requires iterations in calculating the angular velocity at each time step, we propose two kinds of iteration-free fast time-reversible algorithms. They are easily implemented in codes. The codes are compared with that of existing algorithms through demonstrative simulation of a nanometer-sized water droplet to find their stability of the total energy and computation speeds. [ABSTRACT FROM AUTHOR]

We propose a parameter-free algorithm for the identification of nearest neighbors. The algorithm is very easy to use and has a number of advantages over existing algorithms to identify nearest-neighbors. This solid-angle based nearest-neighbor algorithm (SANN) attributes to each possible neighbor a solid angle and determines the cutoff radius by the requirement that the sum of the solid angles is 4π. The algorithm can be used to analyze 3D images, both from experiments as well as theory, and as the algorithm has a low computational cost, it can also be used 'on the fly' in simulations. In this paper, we describe the SANN algorithm, discuss its properties, and compare it to both a fixed-distance cutoff algorithm and to a Voronoi construction by analyzing its behavior in bulk phases of systems of carbon atoms, Lennard-Jones particles and hard spheres as well as in Lennard-Jones systems with liquid-crystal and liquid-vapor interfaces. [ABSTRACT FROM AUTHOR]

Using computer simulations to model the folding of proteins into their native states is computationally expensive due to the extraordinarily low degeneracy of the ground state. In this paper, we develop an efficient way to sample these folded conformations using Wang Landau sampling coupled with the configurational bias method (which uses an unphysical 'temperature' that lies between the collapse and folding transition temperatures of the protein). This method speeds up the folding process by roughly an order of magnitude over existing algorithms for the sequences studied. We apply this method to study the adsorption of intrinsically disordered hydrophobic polar protein fragments on a hydrophobic surface. We find that these fragments, which are unstructured in the bulk, acquire secondary structure upon adsorption onto a strong hydrophobic surface. Apparently, the presence of a hydrophobic surface allows these random coil fragments to fold by providing hydrophobic contacts that were lost in protein fragmentation. [ABSTRACT FROM AUTHOR]

A controlled quantum system possesses a search landscape defined by the target physical objective as a function of the controls. This paper focuses on the landscape for the transition probability Pi → f between the states of a finite level quantum system. Traditionally, the controls are applied fields; here, we extend the notion of control to also include the Hamiltonian structure, in the form of time independent matrix elements. Level sets of controls that produce the same transition probability value are shown to exist at the bottom Pi → f = 0.0 and top Pi → f = 1.0 of the landscape with the field and/or Hamiltonian structure as controls. We present an algorithm to continuously explore these level sets starting from an initial point residing at either extreme value of Pi → f. The technique can also identify control solutions that exhibit the desirable properties of (a) robustness at the top and (b) the ability to rapidly rise towards an optimal control from the bottom. Numerical simulations are presented to illustrate the varied control behavior at the top and bottom of the landscape for several simple model systems. [ABSTRACT FROM AUTHOR]

Density functional theory as proposed by Rosenfeld [Phys. Rev. Lett. 63, 980 (1989)] is used to study hard sphere mixture exposed by cylindrically symmetric external field. Exploiting the symmetry of the system, explicit formulas for the weighted densities are derived. The resulting density profiles are compared with new grand canonical Monte Carlo simulations. The comparison reveals very good agreement between the predicted and simulated results even at high densities and very narrow pores. Finally, simple algorithms for computing complete elliptic functions of the first and second kinds that occur in the derived formulae are presented to make the paper self-contained. [ABSTRACT FROM AUTHOR]

A novel theory of an equation of state based on excluded volume and formulated in two preceding papers for gases and gaseous mixtures is extended to the entire density range by considering higher (beginning from the third) approximations of the theory. The algorithm of constructing higher approximations is elaborated. Equations of state are deduced using the requirement of maximum simplicity and contain a single free parameter to be chosen by reason of convenience or simplicity or to be used as a fitting parameter with respect to the computer simulation database. In this way, precise equations of state are derived for the hard-sphere fluid in the entire density range. On the side, the theory reproduces most known earlier equations of state for hard spheres and determines their place in the hierarchy of approximations. Equations of state for van der Waals fluids are also presented, and their critical parameters are estimated. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this paper, we present computer simulation results concerning interdiffusion of fully compatible components in symmetric binary (AB) polymer mixtures in solutions. The simulation is performed in two dimensions using the algorithm based on the dynamic lattice liquid model. The solvent molecules are taken into account explicitly. The evolution of the concentration profiles in time at an interface is studied for chain lengths N=2,4,8,16 for three polymer concentrations [lowercase_phi_synonym]=0.1,0.5,0.9. The tracer diffusion coefficients for polymer chains and for the solvent are obtained by monitoring the mean square displacements of their center of mass. The relationships between coefficients of interdiffusion and self-diffusion are tested. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]