Table of contents

Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose dynamics are governed by the chemical master equation. Despite its simple structure, no analytic solutions to the chemical master equation are known for most systems. Moreover, stochastic simulations are computationally expensive, making systematic analysis and statistical inference a challenging task. Consequently, significant effort has been spent in recent decades on the development of efficient approximation and inference methods. This article gives an introduction to basic modelling concepts as well as an overview of state of the art methods. First, we motivate and introduce deterministic and stochastic methods for modelling chemical networks, and give an overview of simulation and exact solution methods. Next, we discuss several approximation methods, including the chemical Langevin equation, the system size expansion, moment closure approximations, time-scale separation approximations and hybrid methods. We discuss their various properties and review recent advances and remaining challenges for these methods. We present a comparison of several of these methods by means of a numerical case study and highlight some of their respective advantages and disadvantages. Finally, we discuss the problem of inference from experimental data in the Bayesian framework and review recent methods developed the literature. In summary, this review gives a self-contained introduction to modelling, approximations and inference methods for stochastic chemical kinetics.

100 years after Smoluchowski introduced his approach to stochastic processes, they are now at the basis of mathematical and physical modeling in cellular biology: they are used for example to analyse and to extract features from a large number (tens of thousands) of single molecular trajectories or to study the diffusive motion of molecules, proteins or receptors. Stochastic modeling is a new step in large data analysis that serves extracting cell biology concepts. We review here Smoluchowski's approach to stochastic processes and provide several applications for coarse-graining diffusion, studying polymer models for understanding nuclear organization and finally, we discuss the stochastic jump dynamics of telomeres across cell division and stochastic gene regulation.

Classical and quantum physics provide fundamentally different predictions about experiments with separate observers that do not communicate, a phenomenon known as quantum nonlocality. This insight is a key element of our present understanding of quantum physics, and also enables a number of information processing protocols with security beyond what is classically attainable. Relaxing the pivotal assumption of no communication leads to new insights into the nature quantum correlations, and may enable new applications where security can be established under less strict assumptions. Here, we study such relaxations where different forms of communication are allowed. We consider communication of inputs, outputs, and of a message between the parties. Using several measures, we study how much communication is required for classical models to reproduce quantum or general no-signalling correlations, as well as how quantum models can be augmented with classical communication to reproduce no-signalling correlations.

The recent work by Cardy (arXiv:1603.08267) on quantum revivals and higher dimensional CFT is revisited and enlarged upon for free fields. The expressions for the free energy used here are those derived some time ago. The calculation is extended to spin–half fields for which the power spectrum involves the odd divisor function. An explanation of the rational revivals for odd spheres is given in terms of wrongly quantised fields and modular transformations. Comments are made on the equivalence of operator counting and eigenvalue methods, which is quickly verified.

For disordered interacting quantum systems, the sensitivity of the spectrum to twisted boundary conditions depending on an infinitesimal angle ϕ can be used to analyze the many-body-localization transition. The sensitivity of the energy levels ${{E}_{n}}(\phi )$ is measured by the level curvature ${{K}_{n}}=E_{n}^{\prime \prime}(0)$, or more precisely by the Thouless dimensionless curvature ${{k}_{n}}={{K}_{n}}/{{ \Delta }_{n}}$, where ${{ \Delta }_{n}}$ is the level spacing that decays exponentially with the size L of the system. For instance ${{ \Delta }_{n}}\propto {{2}^{-L}}$ in the middle of the spectrum of quantum spin chains of L spins, while the Drude weight ${{D}_{n}}=L{{K}_{n}}$ studied recently by Filippone et al (arxiv:1606.07291v1) involves a different rescaling. The sensitivity of the eigenstates $|{{\psi}_{n}}(\phi )>$ is characterized by the susceptibility ${{\chi}_{n}}=-F_{n}^{\prime \prime}(0)$ of the fidelity ${{F}_{n}}=\,|<{{\psi}_{n}}(0)|{{\psi}_{n}}(\phi )>|$. Both observables are distributed with probability distributions displaying power-law tails ${{P}_{\beta}}(k)\simeq {{A}_{\beta}}|k{{|}^{-(2+\beta )}}$ and $Q(\chi )\simeq {{B}_{\beta}}{{\chi}^{-\frac{3+\beta}{2}}}$, where β is the level repulsion index taking the values ${{\beta}^{\text{GOE}}}=1$ in the ergodic phase and ${{\beta}^{\text{loc}}}=0$ in the localized phase. The amplitudes ${{A}_{\beta}}$ and ${{B}_{\beta}}$ of these two heavy tails are given by some moments of the off-diagonal matrix element of the local current operator between two nearby energy levels, whose probability distribution has been proposed as a criterion for the many-body-localization transition by Serbyn et al (2015 Phys. Rev. X 5 041047).

We study via Monte Carlo simulation a generalisation of the so-called vertex interacting self-avoiding walk (VISAW) model on the square lattice. The configurations are actually not self-avoiding walks but rather restricted self-avoiding trails (bond avoiding paths) which may visit a site of the lattice twice provided the path does not cross itself: to distinguish this subset of trails we shall call these configurations grooves. Three distinct interactions are added to the configurations: firstly the VISAW interaction, which is associated with doubly visited sites, secondly a nearest neighbour interaction in the same fashion as the canonical interacting self-avoiding walk (ISAW) and thirdly, a stiffness energy to enhance or decrease the probability of bends in the configuration.

In addition to the normal high temperature phase we find three low temperature phases: (i) the usual amorphous liquid drop-like 'globular' phase, (ii) an anisotropic 'β-sheet' phase with dominant configurations consisting of aligned long straight segments, which has been found in semi-flexible nearest neighbour ISAW models, and (iii) a maximally dense phase, where the all sites of the path are associated with doubly visited sites (except those of the boundary of the configuration), previously observed in interacting self-avoiding trails.

We construct a phase diagram using the fluctuations of the energy parameters and three order parameters. The β-sheet and maximally dense phases do not seem to meet in the phase space and are always separated by either the extended or globular phases. We focus attention on the transition between the extended and maximally dense phases, as that is the transition in the original VISAW model. We find that for the path lengths considered there is a range of parameters where the transition is first order and it is otherwise continuous.

Duality relations for simple exclusion processes with general open boundaries are discussed. It is shown that a combination of spin operators and bosonic operators enables us to have a unified discussion about duality relations with open boundaries. As for the symmetric simple exclusion process (SSEP), more general results than those from previous studies are obtained. It is clarified that not only the absorbing sites, but also additional sites—called copying sites— are needed for the boundaries in the dual process for the SSEP. The role of the copying sites is to conserve information about the particle states on the boundary sites. Similar discussions are applied to the asymmetric simple exclusion process (ASEP), in which the q-analogues are employed, and it is clarified that the ASEP with open boundaries has a complicated dual process on the boundaries.

We study the geometry of the space of Mermin pentagrams, objects that are used to rule out the existence of noncontextual hidden variable theories as alternatives to quantum theory. It is shown that this space of 12 096 possible pentagrams is organized into 1008 families, with each family containing a 'double-six' of pentagrams. The 1008 families are connected to a special set of Veldkamp lines in the Veldkamp space for three-qubits an object well-known to finite geometers but has only been introduced to physics recently. Due to the transitive action of the symplectic group on this set of Veldkamp lines it is enough to study only one 'canonical' double-six configuration of pentagrams. We prove that the geometry of this double-six configuration is encapsulated in the weight diagram of the 20 dimensional irreducible representation of the group $\text{SU}(6)$. As an interesting by-product of our approach we show that Mermin pentagrams and a class of Mermin squares labelled by three-qubit Pauli operators are inherently related. We conjecture that by studying the representation theoretic content of other Veldkamp lines of the Veldkamp space for N-qubits makes it possible to find new contextual configurations in a systematic manner.

The Witten–Dijkgraaf–Verlinde–Verlinde (or WDVV) equations, as one would expect from an integrable system, has many symmetries, both continuous and discrete. One class—the so-called Legendre transformations—were introduced by Dubrovin. They are a discrete set of symmetries between the stronger concept of a Frobenius manifold, and are generated by certain flat vector fields. In this paper this construction is generalized to the case where the vector field (called here the Legendre field) is non-flat but satisfies a certain set of defining equations. One application of this more general theory is to generate the induced symmetry between almost-dual Frobenius manifolds whose underlying Frobenius manifolds are related by a Legendre transformation. This also provides a map between rational and trigonometric solutions of the WDVV equations.

Superintegrable systems of 2nd order in 3 dimensions with exactly 3-parameter potentials are intriguing objects. Next to the nondegenerate 4-parameter potential systems they admit the maximum number of symmetry operators, but their symmetry algebras do not close under commutation and not enough is known about their structure to give a complete classification. Some examples are known for which the 3-parameter system can be extended to a 4th order superintegrable system with a 4-parameter potential and 6 linearly independent symmetry generators. In this paper we use Bôcher contractions of the conformal Lie algebra $so\left(5,\mathbb{C}\right)$ to itself to generate a large family of 3-parameter systems with 4th order extensions, on a variety of manifolds, all from Bôcher contractions of a single 'generic' system on the 3-sphere. We give a contraction scheme relating these systems. The results have myriad applications for finding explicit solutions for both quantum and classical systems.

We revisit the problem of interactions of higher-spin fields in flat space. We argue that all no-go theorems can be avoided by the light-cone approach, which results in more interaction vertices as compared to the usual covariant approaches. It is stressed that there exist two-derivative gravitational couplings of higher-spin fields. We show that some reincarnation of the equivalence principle still holds for higher-spin fields—the strength of gravitational interaction does not depend on spin. Moreover, it follows from the results by Metsaev that there exists a complete chiral higher-spin theory in four dimensions. We give a simple derivation of this theory and show that the four-point scattering amplitude vanishes. Also, we reconstruct the quartic vertex of the scalar field in the unitary higher-spin theory, which turns out to be perturbatively local.