arXiv subjects

Thomas R. Sokolowski

Publications and source records attributed to Thomas R. Sokolowski.

12 recordsLinked to original sources

arXiv2025

Initial Luminally Deposited FGF4 Critically Influences Blastocyst Patterning

Luminogenesis, the formation of a fluid-filled cavity (lumen), is an essential process in early mammalian embryonic development, coinciding with the second cell-fate decision that differentiates the inner-cell-mass (ICM) into epiblast (EPI) and primitive endoderm (PRE) tissues. Based on experiments, the blastocyst lumen is hypothesized to influence EPI-PRE tissue specification, but its particular functional role remains theoretically underexplored. In this study, we extended our stochastic ICM differentiation model to incorporate both the blastocyst lumen (blastocoel) and the trophectoderm (TE) as adjacent compartments where the primary signaling protein (FGF4) for EPI-PRE differentiation can diffuse, degrade, or accumulate. This extended ICM model allows for a spatially resolved analysis of EPI-PRE lineage proportioning under the influence of luminally deposited FGF4 molecules. Our results reveal that the blastocoel acts as a localized signaling source, while the TE functions as an embryo-wide signaling sink, guiding cell-fate decisions within the ICM. A critical determinant of the ideal target system behavior is the initial amount of luminally deposited FGF4, which is required to recapitulate the correct spatio-temporal patterning of EPI and PRE (blastocyst) cell lineages. Notably, this requirement is independent of ICM population size and shape, highlighting the robustness of the FGF4 signaling process. Our study also underscores the potential of integrating single-cell gene expression and cell-cell communication dynamics simulations with tissue-level morphogenesis representations. By combining spatial-stochastic modeling with agent-based frameworks, we could enhance the exploration of the intricate interplay between gene regulation, signaling, and morphogenetic processes that govern early embryonic development.

q-bio.QM↗

arXiv2025

Information-Theoretical Measures for Developmental Cell-Fate Proportioning Processes

Self-organization is a fundamental process of complex biological systems, particularly during the early stages of development. In the mammalian embryo, blastocyst formation exemplifies a self-organized system, involving the correct spatio-temporal segregation of three distinct cell fates: trophectoderm (TE), epiblast (EPI), and primitive endoderm (PRE). Despite the significance of this class of processes, quantifying the information content of self-organizing patterning systems remains challenging due to the complexity and the qualitative diversity of developmental mechanisms. In this study, we applied a recently proposed information-theoretical framework which quantifies the self-organization potential of cell-fate patterning systems, employing a utility function that integrates (local) positional information and (global) correlational information extracted from developmental pattern ensembles. Specifically, we examined a stochastic and spatially resolved simulation model of EPI-PRE lineage proportioning, evaluating its information content across various simulation scenarios with different numbers of system cells. To overcome the computational challenges hindering the application of this novel framework, we developed a mathematical strategy that indirectly maps the low-dimensional cell-fate counting probability space to the high-dimensional cell-fate patterning probability space, enabling the estimation of self-organization potential for general cell-fate proportioning processes. Overall, this novel information-theoretical framework provides a promising, universal approach for quantifying self-organization in developmental biology. By formalizing measures of self-organization, the employed quantification framework offers a valuable tool for uncovering insights into the underlying principles of cell-fate specification and the emergence of complexity in early developmental systems.

q-bio.QM↗

arXiv2025

Unifying Physics- and Data-Driven Modeling via Novel Causal Spatiotemporal Graph Neural Network for Interpretable Epidemic Forecasting

Accurate epidemic forecasting is crucial for effective disease control and prevention. Traditional compartmental models often struggle to estimate temporally and spatially varying epidemiological parameters, while deep learning models typically overlook disease transmission dynamics and lack interpretability in the epidemiological context. To address these limitations, we propose a novel Causal Spatiotemporal Graph Neural Network (CSTGNN), a hybrid framework that integrates a Spatio-Contact SIR model with Graph Neural Networks (GNNs) to capture the spatiotemporal propagation of epidemics. Inter-regional human mobility exhibits continuous and smooth spatiotemporal patterns, leading to adjacent graph structures that share underlying mobility dynamics. To model these dynamics, we employ an adaptive static connectivity graph to represent the stable components of human mobility and utilize a temporal dynamics model to capture fluctuations within these patterns. By integrating the adaptive static connectivity graph with the temporal dynamics graph, we construct a dynamic graph that encapsulates the comprehensive properties of human mobility networks. Additionally, to capture temporal trends and variations in infectious disease spread, we introduce a temporal decomposition model to handle temporal dependence. This model is then integrated with a dynamic graph convolutional network for epidemic forecasting. We validate our model using real-world datasets at the provincial level in China and the state level in Germany. Extensive studies demonstrate that our method effectively models the spatiotemporal dynamics of infectious diseases, providing a valuable tool for forecasting and intervention strategies. Furthermore, analysis of the learned parameters offers insights into disease transmission mechanisms, enhancing the interpretability and practical applicability of our model.

cs.LG↗

arXiv2024

Stable developmental patterns of gene expression without morphogen gradients

Gene expression patterns (GEPs) are established by cross-regulating target genes that interpret morphogen gradients. However, as development progresses, morphogen activity is reduced, leaving the emergent GEP without stabilizing positional cues. The GEP then can be deteriorated by the intrinsically noisy biochemical processes acting at the cellular level. However, the established GEPs remain spatio-temporally stable in many biological systems. Here we combine spatial-stochastic simulations with an enhanced sampling method (Non-Stationary Forward Flux Sampling) and a recently developed stability theory to address how spatiotemporal integrity of a GEP is maintained without morphogen gradients. Using a minimal embryo model consisting of spatially coupled biochemical reactor volumes, we study a stripe pattern in which weak cross-repression between nearest neighbor domians alternates with strong repression between next-nearest neighbor domains, inspired by the gap gene system in the Drosophila embryo. We find that fine-tuning of the weak repressive interactions to an optimal level increases temporal stability of GEPs by orders of magnitude, providing stability over developmentally relevant times, without morphogen gradients. The numerically determined optimal parameter regime closely agrees with the predictions of the stability theory. By analizing the dynamics of GEP asymmetry factors, we trace back the pattern stability enhancement to the emergence of a metastable basin and restoring forces that counteract pattern perturbations. The origin of these forces is further explained by the effective model, describing the emergent deterministic dynamics of the system. Altogether, we show that metastable attractors can emerge as a property of stochastic GEPs even without system-wide positional cues, provided that the gene regulatory interactions shaping the pattern are optimally tuned.

physics.bio-ph↗

arXiv2024

Comparing AI versus Optimization Workflows for Simulation-Based Inference of Spatial-Stochastic Systems

Model parameter inference is a universal problem across science. This challenge is particularly pronounced in developmental biology, where faithful mechanistic descriptions require spatial-stochastic models with numerous parameters, yet quantitative empirical data often lack sufficient granularity due to experimental limitations. Parameterizing such complex models thus necessitates methods that elaborate on classical Bayesian inference by incorporating notions of optimality and goal-orientation through low-dimensional objective functions that quantitatively capture the target behavior of the underlying system. In this study, we contrast two such inference workflows and apply them to biophysics-inspired spatial-stochastic models. Technically, both workflows are simulation-based inference (SBI) methods. The first method leverages a modern deep-learning technique known as sequential neural posterior estimation (SNPE), while the second is based on a classical optimization technique called simulated annealing (SA). We evaluate these workflows by inferring the parameters of two complementary models for the inner cell mass (ICM) lineage differentiation in the blastocyst-stage mouse embryo. This developmental biology system serves as a paradigmatic example of a highly robust and reproducible cell-fate proportioning process that self-organizes under strongly stochastic conditions, such as intrinsic biochemical noise and cell-cell signaling delays. Our results indicate that while both methods largely agree in their predictions, the modern SBI workflow provides substantially richer inferred distributions at an equivalent computational cost. We identify the computational scenarios that favor the modern SBI method over its classical counterpart. Finally, we propose a plausible approach to integrate these two methods, thereby synergistically exploiting their parameter space exploration capabilities.

physics.bio-ph↗

arXiv2024

AI-powered simulation-based inference of a genuinely spatial-stochastic model of early mouse embryogenesis

Understanding how multicellular organisms reliably orchestrate cell-fate decisions is a central challenge in developmental biology. This is particularly intriguing in early mammalian development, where early cell-lineage differentiation arises from processes that initially appear cell-autonomous but later materialize reliably at the tissue level. In this study, we develop a multi-scale, spatial-stochastic simulator of mouse embryogenesis, focusing on inner-cell mass (ICM) differentiation in the blastocyst stage. Our model features biophysically realistic regulatory interactions and accounts for the innate stochasticity of the biological processes driving cell-fate decisions at the cellular scale. We advance event-driven simulation techniques to incorporate relevant tissue-scale phenomena and integrate them with Simulation-Based Inference (SBI), building on a recent AI-based parameter learning method: the Sequential Neural Posterior Estimation (SNPE) algorithm. Using this framework, we carry out a large-scale Bayesian inferential analysis and determine parameter sets that reproduce the experimentally observed system behavior. We elucidate how autocrine and paracrine feedbacks via the signaling protein FGF4 orchestrate the inherently stochastic expression of fate-specifying genes at the cellular level into reproducible ICM patterning at the tissue scale. This mechanism is remarkably independent of the system size. FGF4 not only ensures correct cell lineage ratios in the ICM, but also enhances its resilience to perturbations. Intriguingly, we find that high variability in intracellular initial conditions does not compromise, but rather can enhance the accuracy and precision of tissue-level dynamics. Our work provides a genuinely spatial-stochastic description of the biochemical processes driving ICM differentiation and the necessary conditions under which it can proceed robustly.

physics.bio-ph↗

arXiv2019

A Tight Upper Bound on Mutual Information

We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound.

cs.IT↗

arXiv2017

eGFRD in all dimensions

Biochemical reactions typically occur at low copy numbers, but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. However, while particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them oftentimes imply trade-offs between computational efficiency and accuracy. eGFRD (enhanced Green's Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M<N analytically tractable one- and two-particle systems; the analytical solutions (Green's functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at any moment. Here we present "eGFRD2", a new eGFRD version that implements the principle of eGFRD in all dimensions, enabling efficient simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 3 orders of magnitude faster than optimized Brownian Dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent results on this system and demonstrating that it can efficiently operate under genuinely stochastic conditions.

q-bio.MN↗

arXiv2017

Spatial-Stochastic Simulation of Reaction-Diffusion Systems

Biochemical networks play a crucial role in biological systems, implementing a broad range of vital functions. They normally operate at low copy numbers and in spatial settings, but this is often ignored and well-stirred conditions are assumed. Yet, it is increasingly becoming clear that even microscopic spatial inhomogeneities oftentimes can induce significant differences on the macroscopic level. Since experimental observation of single-molecule behavior is extremely challenging, theoretical modeling of biochemical reactions on the single-particle level is an important tool for understanding spatial effects in biochemical systems. While purely analytical models quickly become intractable here, spatial-stochastic simulations can capture a wide range of biochemical processes with the necessary levels of detail. Here we discuss different techniques for spatial-stochastic simulation of reaction-diffusion systems, and explain important precautions required to make them biochemically accurate and efficient. We illustrate non-negligible accuracy issues arising even in the most simple approaches to biochemical simulation, and present methods to deal with them. We first explain how Brownian Dynamics, a widely used particle-based diffusion simulation technique with fixed propagation time, can be adapted to incorporate chemical reactions, and portray a range of schemes that elaborate on this idea. We then introduce event-driven spatial-stochastic simulation methods, in which system updates are performed asynchronously with situation-dependent, varying time steps; here we particularly focus on eGFRD, a computationally efficient particle-based algorithm that makes use of analytical functions to accurately sample interparticle reactions and diffusive motion with large jumps in time and space. We end by briefly presenting recent developments in the field of spatial-stochastic biochemical simulation.

q-bio.MN↗

arXiv2015

Extending the dynamic range of transcription factor action by translational regulation

A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other transcription factors. Intuitively, each mRNA molecule acts as an independent sensor of the TF concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this new scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression.

q-bio.MN↗

arXiv2015

Optimizing information flow in small genetic networks. IV. Spatial coupling

We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.

q-bio.MN↗

arXiv2012

Mutual Repression enhances the Steepness and Precision of Gene Expression Boundaries

Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular, gene expression boundaries are robust not only against intrinsic noise from gene expression and protein diffusion, but also against embryo-to-embryo variations in the morphogen gradients, which provide positional information to the differentiating cells. How development is robust against intra- and inter-embryonic variations is not understood. A common motif in the gene regulation networks that control embryonic development is mutual repression between pairs of genes. To assess the role of mutual repression in the robust formation of gene expression patterns, we have performed large-scale stochastic simulations of a minimal model of two mutually repressing gap genes in Drosophila, hunchback (hb) and knirps (kni). Our model includes not only mutual repression between hb and kni, but also the stochastic and cooperative activation of hb by the anterior morphogen Bicoid (Bcd) and of kni by the posterior morphogen Caudal (Cad), as well as the diffusion of Hb and Kni. Our analysis reveals that mutual repression can markedly increase the steepness and precision of the gap gene expression boundaries. In contrast to spatial averaging and cooperative gene activation, mutual repression thus allows for gene-expression boundaries that are both steep and precise. Moreover, mutual repression dramatically enhances their robustness against embryo-to-embryo variations in the morphogen levels. Finally, our simulations reveal that gap protein diffusion plays a critical role not only in reducing the width of gap gene expression boundaries via spatial averaging, but also in repairing patterning errors that could arise due to the bistability induced by mutual repression.

q-bio.MN↗