arXiv subjects

Kenny Wong

Publications and source records attributed to Kenny Wong.

15 recordsLinked to original sources

arXiv2026

Approximate Analytical Protein Distributions for the Three-stage Model of Stochastic Gene Expression

Gene expression is an intrinsically stochastic process that generates phenotypic heterogeneity within genetically identical cell populations. While the exact statistical moments of the protein count can be obtained for a broad range of complex models, the corresponding distributions are significantly harder to obtain and intractable in many cases. The classical three-stage model of gene expression, which predicts fluctuations in protein levels as a function of promoter switching, transcription, translation, and degradation events all occurring with linear propensities, illustrates this perfectly; deriving its exact protein distribution remains elusive. Here, using the partitioning property of time-inhomogeneous Poisson processes, we develop an exact mapping of the three-stage model onto a simplified model. The simplified model allows us to formulate two analytical approximations for the full protein distribution of the three-stage model based on a beta-mixture representation of the exact solution for a simpler model. We show that the two approximations are asymptotically exact in different limiting cases and verify their accuracy against simulations for a broad range of parameters. Although approximate, these are the first analytical expressions for protein distributions for the three-stage model that are highly accurate in intermediate regimes.

q-bio.QM↗

arXiv2026

Post-transcriptional Regulation of Stochastic Gene Expression Conditioned on Large Deviations

Gene expression is a stochastic process that gives rise to large fluctuations in protein levels leading to phenotypic heterogeneity in clonal cell populations; post-transcriptional regulation plays a crucial role in controlling the level of phenotypic variability within a population, which is directly tied to cell-fate decisions. As such, substantial efforts have been directed towards quantitatively modeling the effects of various post-transcriptional mechanisms on the strength of fluctuations in protein levels (noise). However, the corresponding effects of post-transcriptional regulation on the occurrence of rare events corresponding to large deviations are far less explored and have only been considered for a special model. Here, we take a general model of post-transcriptional regulation and apply the partitioning of Poisson arrivals (PPA) framework to map it onto a model that resembles promoter-based regulation of transcription, leading to a general framework to obtain objects of interest in large deviations (i.e. large deviation rate function for quantifying the likelihood of observing rare protein production rates and the corresponding driven process that characterizes the system dynamics conditional on the rare event) for models of post-transcriptional regulation directly from prior results for promoter-based models. The results derived create new avenues to analyze rare events in general models of post-transcriptional regulation pertaining to various different biological settings.

q-bio.QM↗

arXiv2026

Analyzing Post-transcriptional Regulation in Stochastic Gene Expression Models Using Partitioned Poisson Arrivals

Gene expression is a stochastic process that allows for fluctuations in protein levels that can give rise to phenotypic heterogeneity within a population of genetically identical cells. Thus, there is great interest in quantifying how natural variation (noise) in gene expression is impacted by cellular control mechanisms, such as the various mechanisms pertaining to post-transcriptional regulation. Although previous research has developed a general analytical framework to compute the exact moments of mRNA distributions for any promoter-based regulatory motif, and the exact mRNA distribution itself in some cases, a similar framework for protein fluctuations is currently lacking. Here, we invoke the partitioning property of Poisson arrivals to map a general class of stochastic models of post-transcriptional regulation onto models that resemble promoter-based regulation. This approach leads to exact analytical results for the moments of protein distributions, and in certain cases the full distribution itself, using known exact results for mRNA distributions undergoing arbitrary promoter-based regulation. We further extend the framework to incorporate transcriptional bursting, leading to a versatile, unifying analytical framework for analyzing post-transcriptional regulation in stochastic gene expression.

q-bio.QM↗

arXiv2017

Quarter-BPS states in orbifold sigma models with ADE singularities

We study the elliptic genera of two-dimensional orbifold CFTs, where the orbifolding procedure introduces du Val surface singularities on the target space. The N=4 character decompositions of the elliptic genus contributions from the twisted sectors at the singularities obey a consistent scaling property, and contain information about the arrangement of exceptional rational curves in the resolution. We also discuss how these twisted sector elliptic genera are related to twining genera and Hodge elliptic genera for sigma models with K3 target space.

hep-th↗

arXiv2017

Two-dimensional gauge dynamics and the topology of singular determinantal varieties

We record an observation about the Witten indices in two families of gauged linear sigma models: the U(2) model for linear sections of Grassmannians, and the U(1) model for quadric complete intersections. We describe how the Witten indices are related to the Euler characteristics of the singular skew-symmetric or symmetric determinantal varieties featuring in the analysis of their opposite phases, and we discuss the extent to which these relationships can be reconciled with standard Born-Oppenheimer arguments.

hep-th↗

arXiv2016

Spectral Sequences and Vacua in N = 2 Gauged Linear Quantum Mechanics with Potentials

We study the behaviour of supersymmetric ground states in a class of one-dimensional N = 2 abelian gauged linear sigma models, including theories for which the target space is a complete intersection in projective space, and more generally, models with an interaction term introduced by Herbst, Hori and Page in which the vacua correspond to elements of hypercohomology groups of complexes of sheaves. Combining physical insights from recent work by Hori, Kim and Yi with the use of spectral sequences, we propose a way to reconcile the non-linear sigma model description, valid deep within a geometric phase, with the effective Coulomb branch description, valid near a phase boundary. This leads to a physical interpretation of the hypercohomology groups from the perspective of the Coulomb branch, as well as an interpretation for the spectral sequences used to compute them.

hep-th↗

arXiv2015

Berry's connection, Kähler geometry and the Nahm construction of monopoles

We study supersymmetric deformations of N = 4 quantum mechanics with a Kahler target space admitting a holomorphic isometry. We show that the twisted mass deformation generalises to a deformation constructed from matrix-valued functions of the moment map, which obey the Nahm equations. We also explain how N = 4 supersymmetry implies that the Berry connection on the vacuum bundle for this theory satisfies the BPS monopole equations. In the case where the target space is a Riemann sphere, our analysis reduces to the standard Nahm construction of monopoles. This generalises an earlier result by Sonner and Tong to the case of monopoles of magnetic charge greater than one.

hep-th↗

arXiv2015

ADHM Revisited: Instantons and Wilson Lines

We revisit the well-studied D0-D4 system of D-branes and its relationship to the ADHM construction. It is well known that the D0-branes appear as instantons in the D4-brane worldvolume. We add a Wilson line to the D4-brane in the guise of an extended fundamental string and determine how this affects the D0-brane dynamics. As the D0-brane moves in the presence of the Wilson line, it experiences a Lorentz force, proportional to its Yang-Mills gauge connection. From the perspective of the D0-brane quantum mechanics, this force emerges through the ADHM construction of the self-dual gauge connection.

hep-th↗

arXiv2014

Monopoles and Wilson Lines

We present a semi-classical description of BPS monopoles interacting with Wilson lines. The Wilson lines are represented as non-Abelian spin impurities. These spins interact with the monopole degrees of freedom through a natural connection on the moduli space. We employ this technology in N = 2 SU(2) gauge theory to count the number of framed BPS states of a single monopole bound to Wilson lines in different representations.

hep-th↗

arXiv2014

Vortices and Impurities

We describe the BPS dynamics of vortices in the presence of impurities. We argue that a moduli space of solitons survives the addition of both electric and magnetic impurities. However, dynamics on the moduli space is altered. In the case of electric impurities, the metric remains unchanged but the dynamics is accompanied by a connection term, acting as an effective magnetic field over the moduli space. We give an expression for this connection and compute the vortex-impurity bound states in simple cases. In contrast, magnetic impurities distort the metric on the moduli space. We show that magnetic impurities can be viewed as vortices associated to a second, frozen, gauge group. We provide a D-brane description of the dynamics of vortices in product gauge groups and show how one can take the limit such that a subset of the vortices freeze.

hep-th↗

arXiv2013

A Non-Abelian Vortex Lattice in Strongly Coupled Systems

The AdS/CFT correspondence predicts that background non-abelian magnetic fields induce instabilities in strongly-coupled systems with non-abelian global symmetries. These instabilities lead to the formation of vortex lattices in which the non-abelian currents "antiscreen" the applied magnetic field. From the bulk perspective, this behaviour can be traced to a well-known instability of Yang-Mills theory. We analyse the phase structure of the instability and comment on aspects of the vortex lattice.

hep-th↗

arXiv2013

Gauge Dynamics and Topological Insulators

A non-abelian magnetic field in Yang-Mills theory induces the formation of a "W-boson" vortex lattice. We study the propagation of fundamental fermions in the presence of this lattice in 2+1 dimensions. We show that the spectrum for massless fermions contains four topologically-protected Dirac points with non-zero Bloch momentum. For massive fermions, we compute topological invariants of the band structure and show that it is possible to realise a Z2 topological insulator within Yang-Mills theory.

hep-th↗

arXiv2012

Fluctuation and Dissipation at a Quantum Critical Point

In non-relativistic field theories, quantum fluctuations give rise to dissipative behaviour even at zero temperature. Here we use holographic methods to explore the dissipative dynamics of massive particles coupled to quantum critical theories. We present analytic expressions for correlation functions and response functions. The behaviour changes qualitatively as the dynamical exponent passes through z = 2. In particular, for z > 2, the long time dynamics of the particle is independent of its inertial mass.

hep-th↗

arXiv2012

Holographic Dual of the Lowest Landau Level

We describe the lowest Landau level of a quantum electron star in AdS4. In the presence of a suitably strong magnetic field, the dynamics of fermions in the bulk is effectively reduced from four to two dimensions. These two-dimensional fermions can subsequently be treated using the techniques of bosonization and the difficult many-body problem of building a gravitating, charged quantum star is reduced to solving the sine-Gordon model coupled to a gauge field and a metric. The kinks of the sine-Gordon model provide the holographic dual of the lowest Landau levels of the strongly-coupled d=2+1 dimensional boundary field theory. The system exhibits order one oscillations in the magnetic susceptibility, now arising as a classical effect in the bulk. Moreover, as the chemical potential is varied, we find jumps in the charge density, oscillations in the fractionalised charge density and plateaux in the cohesive charge density

hep-th↗

arXiv2012

A Gapless Hard Wall: Magnetic Catalysis in Bulk and Boundary

We study various aspects of fermions and their chiral condensates, both in the bulk of AdS4 spacetime and in the dual boundary theory. For the most part, we focus on a geometry with an infra-red hard wall. We show that, contrary to common lore, there exist boundary conditions in which the hard wall gives rise to a discrete, but gapless, fermionic spectrum. In such a setting, the presence of a magnetic field induces a bulk fermion condensate which spontaneously breaks CP invariance. We develop the holographic dictionary between composite operators and show that this bulk condensate has the interpretation of boundary magnetic catalysis involving a double-trace operator. Finally, we explain how one can replace the hard wall with bulk magnetic monopoles. In such a framework, magnetic catalysis can be viewed as a consequence of the Callan-Rubakov effect.

hep-th↗