Transition Matrix Monte Carlo Reweighting and Dynamics

We study an induced dynamics in the space of energy of single-spin-flip Monte Carlo algorithm. The method gives an efficient reweighting technique. This dynamics is shown to have relaxation times proportional to the specific heat. Thus, it is plausible for a logarithmic factor in the correlation time of the standard 2D Ising local dynamics.Comment: RevTeX, 5 pages, 3 figure

Exact Markovian kinetic equation for a quantum Brownian oscillator

We derive an exact Markovian kinetic equation for an oscillator linearly coupled to a heat bath, describing quantum Brownian motion. Our work is based on the subdynamics formulation developed by Prigogine and collaborators. The space of distribution functions is decomposed into independent subspaces that remain invariant under Liouville dynamics. For integrable systems in Poincar\'e's sense the invariant subspaces follow the dynamics of uncoupled, renormalized particles. In contrast for non-integrable systems, the invariant subspaces follow a dynamics with broken-time symmetry, involving generalized functions. This result indicates that irreversibility and stochasticity are exact properties of dynamics in generalized function spaces. We comment on the relation between our Markovian kinetic equation and the Hu-Paz-Zhang equation.Comment: A few typos in the published version are correcte

The rigged Hilbert space approach to the Lippmann-Schwinger equation. Part II: The analytic continuation of the Lippmann-Schwinger bras and kets

The analytic continuation of the Lippmann-Schwinger bras and kets is obtained and characterized. It is shown that the natural mathematical setting for the analytic continuation of the solutions of the Lippmann-Schwinger equation is the rigged Hilbert space rather than just the Hilbert space. It is also argued that this analytic continuation entails the imposition of a time asymmetric boundary condition upon the group time evolution, resulting into a semigroup time evolution. Physically, the semigroup time evolution is simply a (retarded or advanced) propagator.Comment: 32 pages, 3 figure

Antigen receptor repertoires of one of the smallest known vertebrates

The rules underlying the structure of antigen receptor repertoires are not yet fully defined, despite their enormous importance for the understanding of adaptive immunity. With current technology, the large antigen receptor repertoires of mice and humans cannot be comprehensively studied. To circumvent the problems associated with incomplete sampling, we have studied the immunogenetic features of one of the smallest known vertebrates, the cyprinid fish Paedocypris sp. “Singkep” (“minifish”). Despite its small size, minifish has the key genetic facilities characterizing the principal vertebrate lymphocyte lineages. As described for mammals, the frequency distributions of immunoglobulin and T cell receptor clonotypes exhibit the features of fractal systems, demonstrating that self-similarity is a fundamental property of antigen receptor repertoires of vertebrates, irrespective of body size. Hence, minifish achieve immunocompetence via a few thousand lymphocytes organized in robust scale-free networks, thereby ensuring immune reactivity even when cells are lost or clone sizes fluctuate during immune responses

On the Thermal Symmetry of the Markovian Master Equation

The quantum Markovian master equation of the reduced dynamics of a harmonic oscillator coupled to a thermal reservoir is shown to possess thermal symmetry. This symmetry is revealed by a Bogoliubov transformation that can be represented by a hyperbolic rotation acting on the Liouville space of the reduced dynamics. The Liouville space is obtained as an extension of the Hilbert space through the introduction of tilde variables used in the thermofield dynamics formalism. The angle of rotation depends on the temperature of the reservoir, as well as the value of Planck's constant. This symmetry relates the thermal states of the system at any two temperatures. This includes absolute zero, at which purely quantum effects are revealed. The Caldeira-Leggett equation and the classical Fokker-Planck equation also possess thermal symmetry. We compare the thermal symmetry obtained from the Bogoliubov transformation in related fields and discuss the effects of the symmetry on the shape of a Gaussian wave packet.Comment: Eqs.(64a), (65a)-(68) are correcte

Predictability of large future changes in a competitive evolving population

The dynamical evolution of many economic, sociological, biological and physical systems tends to be dominated by a relatively small number of unexpected, large changes (`extreme events'). We study the large, internal changes produced in a generic multi-agent population competing for a limited resource, and find that the level of predictability actually increases prior to a large change. These large changes hence arise as a predictable consequence of information encoded in the system's global state.Comment: 10 pages, 3 figure

Isostatic phase transition and instability in stiff granular materials

In this letter, structural rigidity concepts are used to understand the origin of instabilities in granular aggregates. It is shown that: a) The contact network of a noncohesive granular aggregate becomes exactly isostatic in the limit of large stiffness-to-load ratio. b) Isostaticity is responsible for the anomalously large susceptibility to perturbation of these systems, and c) The load-stress response function of granular materials is critical (power-law distributed) in the isostatic limit. Thus there is a phase transition in the limit of intinitely large stiffness, and the resulting isostatic phase is characterized by huge instability to perturbation.Comment: RevTeX, 4 pages w/eps figures [psfig]. To appear in Phys. Rev. Let

Dynamics of Fluid Vesicles in Oscillatory Shear Flow

The dynamics of fluid vesicles in oscillatory shear flow was studied using differential equations of two variables: the Taylor deformation parameter and inclination angle $\theta$. In a steady shear flow with a low viscosity $\eta_{\rm {in}}$ of internal fluid, the vesicles exhibit steady tank-treading motion with a constant inclination angle $\theta_0$. In the oscillatory flow with a low shear frequency, $\theta$ oscillates between $\pm \theta_0$ or around $\theta_0$ for zero or finite mean shear rate $\dot\gamma_{\rm m}$, respectively. As shear frequency $f_{\gamma}$ increases, the vesicle oscillation becomes delayed with respect to the shear oscillation, and the oscillation amplitude decreases. At high $f_{\gamma}$ with $\dot\gamma_{\rm m}=0$, another limit-cycle oscillation between $\theta_0-\pi$ and $-\theta_0$ is found to appear. In the steady flow, $\theta$ periodically rotates (tumbling) at high $\eta_{\rm {in}}$, and $\theta$ and the vesicle shape oscillate (swinging) at middle $\eta_{\rm {in}}$ and high shear rate. In the oscillatory flow, the coexistence of two or more limit-cycle oscillations can occur for low $f_{\gamma}$ in these phases. For the vesicle with a fixed shape, the angle $\theta$ rotates back to the original position after an oscillation period. However, it is found that a preferred angle can be induced by small thermal fluctuations.Comment: 11 pages, 13 figure

Multi-Particle Collision Dynamics -- a Particle-Based Mesoscale Simulation Approach to the Hydrodynamics of Complex Fluids

In this review, we describe and analyze a mesoscale simulation method for fluid flow, which was introduced by Malevanets and Kapral in 1999, and is now called multi-particle collision dynamics (MPC) or stochastic rotation dynamics (SRD). The method consists of alternating streaming and collision steps in an ensemble of point particles. The multi-particle collisions are performed by grouping particles in collision cells, and mass, momentum, and energy are locally conserved. This simulation technique captures both full hydrodynamic interactions and thermal fluctuations. The first part of the review begins with a description of several widely used MPC algorithms and then discusses important features of the original SRD algorithm and frequently used variations. Two complementary approaches for deriving the hydrodynamic equations and evaluating the transport coefficients are reviewed. It is then shown how MPC algorithms can be generalized to model non-ideal fluids, and binary mixtures with a consolute point. The importance of angular-momentum conservation for systems like phase-separated liquids with different viscosities is discussed. The second part of the review describes a number of recent applications of MPC algorithms to study colloid and polymer dynamics, the behavior of vesicles and cells in hydrodynamic flows, and the dynamics of viscoelastic fluids