Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons of enormous relevance underlying the protein folding problem and summarize the present-day status of the methods aimed at solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the ‘special flavour’ of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.     

An introduction to multi-GPU programming for physicists

We present and compare different approaches for using multiple Graphics Processing Units in the simulation of physical systems. As benchmarks we consider the time required to update a single spin of the 3D Heisenberg spin glass model, by using both the Over-relaxation and the Heat Bath algorithms, and the solution of a Poisson equation by using a finite-difference method. The results show that a suitable combination of techniques allows to hide almost completely the communication overhead by using the CPU as a communication coprocessor of the GPU. Large scale simulations on clusters of GPUs can be efficiently carried out by following the same approach for other applications where a clear cut exists between bulk and boundaries data.     

Algebraic dynamics solution to and algebraic dynamics algorithm for nonlinear advection equation

Algebraic dynamics approach and algebraic dynamics algorithm for the solution of nonlinear partial differential equations are applied to the nonlinear advection equation. The results show that the approach is effective for the exact analytical solution and the algorithm has higher precision than other existing algorithms in numerical computation for the nonlinear advection equation. Supported by the National Natural Science Foundation of China (Grant Nos. 90503008 and 10775100), the Doctoral Program Foundation from the Ministry of Education of China, and the Center of Theoretical Nuclear Physics of HIRFL of China     

SLE for theoretical physicists

This article provides an introduction to Schramm (stochastic)-Loewner evolution (SLE) and to its connection with conformal field theory, from the point of view of its application to two-dimensional critical behaviour. The emphasis is on the conceptual ideas rather than rigorous proofs.     

Topological quantum mechanics for physicists

This text is an attempt to write an introduction and outline of main results of topological quantum mechanics for readers with a physical background. Instead of presenting rigorous mathematical formulations, we concentrate on explanation of the physical ideas that underline most of the constructions. We review here topological quantum mechanics, since it is the simplest in the diverse family of topological theories, which contains most of their common properties.     

Scientific realism: A challenge to physicists

If a physicist claims to be a realist, he or she must face at least the three problems outlined here: the careful specification of the validity limits of every theory and model used, the coherence relationships that must hold between two theories of the same physical system but on different cognitive levels, and the ambiguity in the ontology of two different formulations of empirically equivalent theories.This paper is dedicated to Professor Max Jammer in honor of his eightieth birthday. I have learned a great deal from his many excellent papers and books in history and philosophy of physics. Thank you and congratulations!     

Exact dynamics for fully connected nonlinear networks

We investigate the dynamics of the discrete nonlinear Schrödinger equation in fully connected networks. For a localized initial condition the exact solution shows the existence of two dynamical transitions as a function of the nonlinearity parameter, a hyperbolic and a trigonometric one. In the latter the network behaves exactly as the corresponding linear one but with a renormalized frequency.     

A nonlinear dynamics method for signal identification

When a radio frequency signal is radiated by a transmitter, the properties of the transmitter itself affect the properties of the signal. These transmitter-induced changes are known as unintentional modulation, to differentiate them from intentional modulation used to add information to the signal. The unintentional modulation can be used to identify which transmitter produced a signal. This paper shows how phase space analysis based on nonlinear dynamics ideas can be used to determine which of several amplifiers produced a signal.     

Remarkable physicists: from Galileo to Yukawa

Electrical conduction in ultra-thin metal films is examined and the part played by an anomalous quantum mechanical tunnelling process is investigated. The process varies greatly with temperature, because the discrete metal particles forming the film are very small. The work required to remove a charge from such a particle being an inverse function of the particle size.

The nature of the conduction path between the metal particles is considered, and it is shown that conduction occurs through the substrate supporting the film. Experimental results for gold, platinum end chromium films on soda and alumino-borosilicate glasses are analysed in terms of a proposed model. The consistency of the values of the barrier heights between the metal particles and the glass substrate, supports the quantum mechanical tunnelling model.     

Chaos without nonlinear dynamics

A linear, second-order filter driven by randomly polarized pulses is shown to generate a waveform that is chaotic under time reversal. That is, the filter output exhibits determinism and a positive Lyapunov exponent when viewed backward in time. The filter is demonstrated experimentally using a passive electronic circuit, and the resulting waveform exhibits a Lorenz-like butterfly structure. This phenomenon suggests that chaos may be connected to physical theories whose underlying framework is not that of a traditional deterministic nonlinear dynamical system.     

On nonlinear coherent states properties for electron-phonon dynamics

This work addresses a construction of a dual pair of nonlinear coherent states (NCS) in the context of changes of bases in the underlying Hilbert space for a model pertaining to an electron-phonon model in the condensed matter physics, obeying a f-deformed Heisenberg algebra. The existence and properties of reproducing kernel in the NCS Hilbert space are studied and discussed; the probability density and its dynamics in the basis of constructed coherent states are provided. A Glauber-Sudarshan P-representation of the density matrix and relevant issues related to the reproducing kernel properties are presented. Moreover, a NCS quantization of classical phase space observables is performed and illustrated in a concrete example of q-deformed coherent states. Finally, an exposition of quantum optical properties is given.     

New approach to nonlinear dynamics of fullerenes and fullerites

A new type of nonlinear (anharmonic) excitations—bushes of vibrational modes—in physical systems with point or space symmetry is discussed. All infrared-active and Raman-active bushes for C₆₀ fullerene are found by means of special group-theoretical methods.