Comment on "Critique and correction of the currently accepted solution of the infinite spherical well in quantum mechanics" by Huang Young-Sea and Thomann Hans-Rudolph

We comment on the paper "Critique and correction of the currently accepted solution of the infinite spherical well in quantum mechanics" by Huang Young-Sea and Thomann Hans-Rudolph, EPL 115, 60001 (2016) .Comment: 2 pages; Submitted to the Comments Section of EP

Understanding the dependence on the pulling speed of the unfolding pathway of proteins

The dependence of the unfolding pathway of proteins on the pulling speed is investigated. This is done by introducing a simple one-dimensional chain comprising $N$ units, with different characteristic bistable free energies. These units represent either each of the modules in a modular protein or each of the intermediate "unfoldons" in a protein domain, which can be either folded or unfolded. The system is pulled by applying a force to the last unit of the chain, and the units unravel following a preferred sequence. We show that the unfolding sequence strongly depends on the pulling velocity $v_{p}$. In the simplest situation, there appears a critical pulling speed $v_{c}$: for pulling speeds $v_{p}v_{c}$ it is the pulled unit that unfolds first. By means of a perturbative expansion, we find quite an accurate expression for this critical velocity.Comment: accepted for publication in JSTA

Lattice models for granular-like velocity fields: Finite-size effects

Long-range spatial correlations in the velocity and energy fields of a granular fluid are discussed in the framework of a 1d lattice model. The dynamics of the velocity field occurs through nearest-neighbour inelastic collisions that conserve momentum but dissipate energy. A set of equations for the fluctuating hydrodynamics of the velocity and energy mesoscopic fields give a first approximation for (i) the velocity structure factor and (ii) the finite-size correction to the Haff law, both in the homogeneous cooling regime. At a more refined level, we have derived the equations for the two-site velocity correlations and the total energy fluctuations. First, we seek a perturbative solution thereof, in powers of the inverse of system size. On the one hand, when scaled with the granular temperature, the velocity correlations tend to a stationary value in the long time limit. On the other hand, the scaled standard deviation of the total energy diverges, that is, the system shows multiscaling. Second, we find an exact solution for the velocity correlations in terms of the spectrum of eigenvalues of a certain matrix. The results of numerical simulations of the microscopic model confirm our theoretical results, including the above described multiscaling phenomenon

Finite-time adiabatic processes: derivation and speed limit

Obtaining adiabatic processes that connect equilibrium states in a given time represents a challenge for mesoscopic systems. In this paper, we explicitly show how to build these finite-time adiabatic processes for an overdamped Brownian particle in an arbitrary potential, a system that is relevant both at the conceptual and the practical level. This is achieved by jointly engineering the time evolutions of the binding potential and the fluid temperature. Moreover, we prove that the second principle imposes a speed limit for such adiabatic transformations: there appears a minimum time to connect the initial and final states. This minimum time can be explicitly calculated for a general compression/decompression situation.Comment: Main text: 5 pages; 18 pages with appendices and references; major revision with results for a general non-linear potential and study of fluctuations added; Physical Review E in pres

Photoproduction total cross section and shower development

The total photoproduction cross section at ultra-high energies is obtained using a model based on QCD minijets and soft-gluon resummation and the ansatz that infrared gluons limit the rise of total cross sections. This cross section is introduced into the Monte Carlo system AIRES to simulate extended air-showers initiated by cosmic ray photons. The impact of the new photoproduction cross section on common shower observables, especially those related to muon production, is compared with previous results

Non-equilibrium memory effects: granular fluids and beyond

In this perspective paper, we look into memory effects in out-of-equilibrium systems. To be concrete, we exemplify memory effects with the paradigmatic case of granular fluids, although extensions to other contexts such as molecular fluids with non-linear drag are also considered. The focus is put on two archetypal memory effects: the Kovacs and Mpemba effects. In brief, the first is related to imperfectly reaching a steady state -- either equilibrium or non-equilibrium, whereas the second is related to reaching a steady state faster despite starting further. Connections to optimal control theory thus naturally emerge and are briefly discussed.Comment: Perspective paper for EPL, 7 pages, 6 figure

Modelling the unfolding pathway of biomolecules: theoretical approach and experimental prospect

We analyse the unfolding pathway of biomolecules comprising several independent modules in pulling experiments. In a recently proposed model, a critical velocity $v_{c}$ has been predicted, such that for pulling speeds $v>v_{c}$ it is the module at the pulled end that opens first, whereas for $v<v_{c}$ it is the weakest. Here, we introduce a variant of the model that is closer to the experimental setup, and discuss the robustness of the emergence of the critical velocity and of its dependence on the model parameters. We also propose a possible experiment to test the theoretical predictions of the model, which seems feasible with state-of-art molecular engineering techniques.Comment: Accepted contribution for the Springer Book "Coupled Mathematical Models for Physical and Biological Nanoscale Systems and Their Applications" (proceedings of the BIRS CMM16 Workshop held in Banff, Canada, August 2016), 16 pages, 6 figure

Ionization via Chaos Assisted Tunneling

A simple example of quantum transport in a classically chaotic system is studied. It consists in a single state lying on a regular island (a stable primary resonance island) which may tunnel into a chaotic sea and further escape to infinity via chaotic diffusion. The specific system is realistic : it is the hydrogen atom exposed to either linearly or circularly polarized microwaves. We show that the combination of tunneling followed by chaotic diffusion leads to peculiar statistical fluctuation properties of the energy and the ionization rate, especially to enhanced fluctuations compared to the purely chaotic case. An appropriate random matrix model, whose predictions are analytically derived, describes accurately these statistical properties.Comment: 30 pages, 11 figures, RevTeX and postscript, Physical Review E in pres

Non-human TRIM5 variants enhance recognition of HIV-1-infected cells by CD8+ T cells

Tripartite motif-containing protein 5 (TRIM5) restricts human immunodeficiency virus type-1 (HIV-1) in a species-specific manner by uncoating viral particles while activating early innate responses. Although the contribution of TRIM5 proteins to cellular immunity has not yet been studied, their interactions with the incoming viral capsid and the cellular proteasome led us to hypothesize a role for them. Here, we investigate whether the expression of two non-human TRIM5 orthologs, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), both of which are potent restrictors of HIV-1, could enhance immune recognition of infected cells by CD8+ T cells. We illustrate how TRIM5 restriction improves CD8+ T cell-mediated HIV-1 inhibition. Moreover, when TRIM5 activity was blocked by the non-immunosuppressive analog of cyclosporin A, SmBz-CsA, we found a significant reduction in CD107a/MIP1β expression in HIV-1-specific CD8+ T cells. This finding underscores the direct link between TRIM5 restriction and activation of CD8+ T-cell responses. Interestingly, cells expressing RhT5 induced stronger CD8+ T-cell responses through the specific recognition of the HIV-1 capsid by the immune system. The underlying mechanism of this process may involve TRIM5-specific capsid recruitment to cellular proteasomes and increase peptide availability for loading and presentation of HLA class I antigens. In summary, we identified a novel function for non-human TRIM5 variants in cellular immunity. We hypothesise that TRIM5 can couple innate viral sensing and CD8+ T-cell activation to increase species barriers against retrovirus infection. IMPORTANCE: New therapeutics to tackle HIV-1 infection should aim to combine rapid innate viral sensing and cellular immune recognition. Such strategies could prevent seeding of the viral reservoir and the immune damage that occurs during acute infection. The non-human TRIM5 variants, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), are attractive candidates owing to their potency in sensing HIV-1 and blocking its activity. Here, we show that expression of RhT5 and TCyp in HIV-1-infected cells improves CD8+ T cell-mediated inhibition through the direct activation of HIV-1-specific CD8+ T-cell responses. We found that the potency in CD8+ activation was stronger for RhT5 variants and capsid-specific CD8+ T-cells in a mechanism that relies on TRIM5-dependent particle recruitment to cellular proteasomes. This novel mechanism couples innate viral sensing with cellular immunity in a single protein and could be exploited to develop innovative therapeutics for control of HIV-1 infection