Entropy driven key-lock assembly

The effective interaction between a sphere with an open cavity (lock) and a spherical macroparticle (key), both immersed in a hard sphere fluid, is studied by means of Monte Carlo simulations. As a result, a 2d map of the key-lock effective interaction potential is constructed, which leads to the proposal of a self-assembling mechanism: there exists trajectories through which the key-lock pair could assemble avoiding trespassing potential barriers. Hence, solely the entropic contribution can induce their self-assembling even in the absence of attractive forces. This study points out the solvent contribution within the underlying mechanisms of substrate-protein assembly/disassembly processes, which are important steps of the enzyme catalysis and protein mediated transport

Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics

Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems the inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems, their basic properties allow to understand fundamental dynamical properties of complex biological reaction networks. We analyze the Lyapunov spectrum, determine the probability to find stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network and study how the frequency distributions of oscillatory modes of such system depend on the average connectivity.Comment: 11 pages, 5 figure

Classification of All Poisson-Lie Structures on an Infinite-Dimensional Jet Group

A local classification of all Poisson-Lie structures on an infinite-dimensional group $G_{\infty}$ of formal power series is given. All Lie bialgebra structures on the Lie algebra {\Cal G}_{\infty} of $G_{\infty}$ are also classified.Comment: 11 pages, AmSTeX fil

Stub model for dephasing in a quantum dot

As an alternative to Buttiker's dephasing lead model, we examine a dephasing stub. Both models are phenomenological ways to introduce decoherence in chaotic scattering by a quantum dot. The difference is that the dephasing lead opens up the quantum dot by connecting it to an electron reservoir, while the dephasing stub is closed at one end. Voltage fluctuations in the stub take over the dephasing role from the reservoir. Because the quantum dot with dephasing lead is an open system, only expectation values of the current can be forced to vanish at low frequencies, while the outcome of an individual measurement is not so constrained. The quantum dot with dephasing stub, in contrast, remains a closed system with a vanishing low-frequency current at each and every measurement. This difference is a crucial one in the context of quantum algorithms, which are based on the outcome of individual measurements rather than on expectation values. We demonstrate that the dephasing stub model has a parameter range in which the voltage fluctuations are sufficiently strong to suppress quantum interference effects, while still being sufficiently weak that classical current fluctuations can be neglected relative to the nonequilibrium shot noise.Comment: 8 pages with 1 figure; contribution for the special issue of J.Phys.A on "Trends in Quantum Chaotic Scattering

Hamiltonian type Lie bialgebras

We first prove that, for any generalized Hamiltonian type Lie algebra $L$, the first cohomology group $H^1(L,L \otimes L)$ is trivial. We then show that all Lie bialgebra structures on $L$ are triangular.Comment: LaTeX, 16 page

Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24.

Off-target binding of hydrophobic drugs can lead to unwanted side effects, either through specific or non-specific binding to unintended membrane protein targets. However, distinguishing the binding of drugs to membrane proteins from that of detergents, lipids and cofactors is challenging. Here, we use high-resolution mass spectrometry to study the effects of HIV protease inhibitors on the human zinc metalloprotease ZMPSTE24. This intramembrane protease plays a major role in converting prelamin A to mature lamin A. We monitored the proteolysis of farnesylated prelamin A peptide by ZMPSTE24 and unexpectedly found retention of the C-terminal peptide product with the enzyme. We also resolved binding of zinc, lipids and HIV protease inhibitors and showed that drug binding blocked prelamin A peptide cleavage and conferred stability to ZMPSTE24. Our results not only have relevance for the progeria-like side effects of certain HIV protease inhibitor drugs, but also highlight new approaches for documenting off-target drug binding

Controlling Nanowire Growth by Light.

Individual Au catalyst nanoparticles are used for selective laser-induced chemical vapor deposition of single germanium nanowires. Dark-field scattering reveals in real time the optical signatures of all key constituent growth processes. Growth is initially triggered by plasmonic absorption in the Au catalyst, while once nucleated the growing Ge nanowire supports magnetic and electric resonances that then dominate the laser interactions. This spectroscopic understanding allows real-time laser feedback that is crucial toward realizing the full potential of controlling nanomaterial growth by light.We acknowledge financial support from EPSRC Grant EP/G060649/1, EP/L027151/1, EP/G037221/1, EPSRC NanoDTC, and ERC Grant LINASS 320503. S.H. acknowledges funding from ERC Grant InsituNANO 279342.This is the author accepted manuscript. The final version is available from ACS via http://dx.doi.org/10.1021/acs.nanolett.5b0295

Phase-Locked Spatial Domains and Bloch Domain Walls in Type-II Optical Parametric Oscillators

We study the role of transverse spatial degrees of freedom in the dynamics of signal-idler phase locked states in type-II Optical Parametric Oscillators. Phase locking stems from signal-idler polarization coupling which arises if the cavity birefringence and/or dichroism is not matched to the nonlinear crystal birefringence. Spontaneous Bloch domain wall formation is theoretically predicted and numerically studied. Bloch walls connect, by means of a polarization transformation, homogeneous regions of self-phase locked solutions. The parameter range for their existence is analytically found. The polarization properties and the dynamics of walls in one- and two transverse spatial dimensions is explained. Transition from Bloch to Ising walls is characterized, the control parameter being the linear coupling strength. Wall dynamics governs spatiotemporal dynamical states of the system, which include transient curvature driven domain growth, persistent dynamics dominated by spiraling defects for Bloch walls, and labyrinthine pattern formation for Ising walls.Comment: 27 pages, 16 figure