arXiv subjects

Nils-Ole Walliser

Publications and source records attributed to Nils-Ole Walliser.

10 recordsLinked to original sources

arXiv2026

Equilibrium cluster statistics of cooperative and anticooperative binding on finite one-dimensional rings

We study equilibrium clustering in a finite one-dimensional lattice gas of $L$ sites with periodic boundary conditions, as a minimal model for adsorption and binding on small ring-like substrates. Using a grand-canonical formulation with nearest-neighbor coupling, we derive exact finite-size expressions for the mean occupancy, the mean number of domain walls, and the mean number of clusters. Building on exact $k$-site correlation functions, we further derive expressions for the mean number of clusters of size $k$ and for two complementary size statistics: the cluster-size distribution, and the site-weighted cluster-size distribution. These observables characterize how spatial organization changes across attractive (cooperative) and repulsive (anticooperative) interactions, and highlight finite-size and parity-dependent effects of the underlying lattice, the latter being particularly pronounced near half filling in small systems. To access larger lattices without enumerating all $2^L$ microstates, we also develop a cluster-based combinatorial formulation in which configurations are classified by cluster counts and sizes, reducing the effective state space to a set whose size scales with integer partitions, $\approx e^{\sqrt{L}}$, rather than with $\approx e^{L}$. Taken together, our results provide exact benchmarks for finite periodic systems and suggest experimentally relevant cluster observables that complement occupancy-based measures of cooperativity, with particular relevance for binding on ring-like substrates for biological assemblies.

cond-mat.stat-mech↗

arXiv2024

Signature of (anti)cooperativity in the stochastic fluctuations of small systems: application to the bacterial flagellar motor

The cooperative binding of molecular agents onto a substrate is pervasive in living systems. To study whether a system shows cooperativity, one can rely on a fluctuation analysis of quantities such as the number of substrate-bound units and the residence time in an occupancy state. Since the relative standard deviation from the statistical mean monotonically decreases with the number of binding sites, these techniques are only suitable for small enough systems, such as those implicated in stochastic processes inside cells. Here, we present a general-purpose grand canonical Hamiltonian description of a small one-dimensional (1D) lattice gas with either nearest-neighbor or long-range interactions as prototypical examples of cooperativity-influenced adsorption processes. First, we elucidate how the strength and sign of the interaction potential between neighboring bound particles on the lattice determine the intensity of the fluctuations of the mean occupancy. We then employ this relationship to compare the theoretical predictions of our model to data from single molecule experiments on bacterial flagellar motors (BFM) of E. coli. In this way, we find evidence that cooperativity controls the mechano-sensitive dynamical assembly of the torque-generating units, the so-called stator units, onto the BFM. Furthermore, in an attempt to quantify fluctuations and the adaptability of the BFM, we estimate the stator-stator interaction potential. Finally, we conclude that the system resides in a sweet spot of the parameter space (phase diagram) suitable for a smoothly adaptive system while minimizing fluctuations.

physics.bio-ph↗

arXiv2023

Chain decay and rates disorder in the totally asymmetric simple exclusion process

We theoretically study the Totally Asymmetric Exclusion Process (TASEP) with quenched jumping rates disorder and finite lifetime chain. TASEP is widely used to model the translation of messenger RNAs by Ribosomes in protein synthesis. Since the exact solution of the TASEP model is analytically and computationally intractable for biologically relevant systems parameters, the canonical Mean-Field (MF) approaches of solving coupled non-linear differential equations is also computational expensive for the scale of relevant biological data analysis. In this article, we provide alternative approach to computing the MF steady state solution via a computationally efficient system of non-linear algebraic equations. We further outline a framework for including correlations progressively via the exact solution of small size TASEP system. Leading order approximation in the biologically relevant entry rate limited regime shows remarkable agreement with the full Monte-Carlo simulation result for a wide range of system parameter space. These results could be of importance to the kinetic rates inference in Ribo-Seq data analysis and other related problems.

cond-mat.stat-mech↗

arXiv2022

Physical modeling of ribosomes along messenger RNA: estimating kinetic parameters from ribosome profiling experiments using a ballistic model

Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes onto mRNA. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criteria for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.

physics.bio-ph↗

arXiv2017

Looping and Clustering model for the organization of protein-DNA complexes on the bacterial genome

The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. With this approach we consider the genomic organization of such a protein-DNA cluster around a single high-affinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate (parS) binding site.

physics.bio-ph↗

arXiv2012

PALP - a User Manual

This article provides a complete user's guide to version 2.1 of the toric geometry package PALP by Maximilian Kreuzer and others. In particular, previously undocumented applications such as the program nef.x are discussed in detail. New features of PALP 2.1 include an extension of the program mori.x which can now compute Mori cones and intersection rings of arbitrary dimension and can also take specific triangulations of reflexive polytopes as input. Furthermore, the program nef.x is enhanced by an option that allows the user to enter reflexive Gorenstein cones as input. The present documentation is complemented by a Wiki which is available online.

math.AG↗

arXiv2011

Restrictions on infinite sequences of type IIB vacua

Ashok and Douglas have shown that infinite sequences of type IIB flux vacua with imaginary self-dual flux can only occur in so-called D-limits, corresponding to singular points in complex structure moduli space. In this work we refine this no-go result by demonstrating that there are no infinite sequences accumulating to the large complex structure point of a certain class of one-parameter Calabi-Yau manifolds. We perform a similar analysis for conifold points and for the decoupling limit, obtaining identical results. Furthermore, we establish the absence of infinite sequences in a D-limit corresponding to the large complex structure limit of a two-parameter Calabi-Yau. In particular, our results demonstrate analytically that the series of vacua recently discovered by Ahlqvist et al., seemingly accumulating to the large complex structure point, are finite. We perform a numerical study of these series close to the large complex structure point using appropriate approximations for the period functions. This analysis reveals that the series bounce out from the large complex structure point, and that the flux eventually ceases to be imaginary self-dual. Finally, we study D-limits for F-theory compactifications on K3\times K3 for which the finiteness of supersymmetric vacua is already established. We do find infinite sequences of flux vacua which are, however, identified by automorphisms of K3.

hep-th↗

arXiv2011

A new offspring of PALP

We describe the C program mori.x. It is part of PALP, a package for analyzing lattice polytopes. Its main purpose is the construction and analysis of three--dimensional smooth Calabi--Yau hypersurfaces in toric varieties. The ambient toric varieties are given in terms of fans over the facets of reflexive lattice polytopes. The program performs crepant star triangulations of reflexive polytopes and determines the Mori cones of the resulting toric varieties. Furthermore, it computes the intersection rings and characteristic classes of hypersurfaces.

math.AG↗

arXiv2011

Toric Construction of Global F-Theory GUTs

We systematically construct a large number of compact Calabi-Yau fourfolds which are suitable for F-theory model building. These elliptically fibered Calabi-Yaus are complete intersections of two hypersurfaces in a six dimensional ambient space. We first construct three-dimensional base manifolds that are hypersurfaces in a toric ambient space. We search for divisors which can support an F-theory GUT. The fourfolds are obtained as elliptic fibrations over these base manifolds. We find that elementary conditions which are motivated by F-theory GUTs lead to strong constraints on the geometry, which significantly reduce the number of suitable models. The complete database of models is available at http://hep.itp.tuwien.ac.at/f-theory/. We work out several examples in more detail.

hep-th↗

arXiv2009

Four-modulus "Swiss Cheese" chiral models

We study the 'Large Volume Scenario' on explicit, new, compact, four-modulus Calabi-Yau manifolds. We pay special attention to the chirality problem pointed out by Blumenhagen, Moster and Plauschinn. Namely, we thoroughly analyze the possibility of generating neutral, non-perturbative superpotentials from Euclidean D3-branes in the presence of chirally intersecting D7-branes. We find that taking proper account of the Freed-Witten anomaly on non-spin cycles and of the Kaehler cone conditions imposes severe constraints on the models. Nevertheless, we are able to create setups where the constraints are solved, and up to three moduli are stabilized.

hep-th↗