Aug 2026· Zenodo (CERN European Organization for Nuclear Research)
Gene Regulatory Network Analysis
Abstract
This paper proposes a novel approach to simulating complex biological systems utilizing graph-based modeling and simulation techniques. The core claim is that traditional simulation methods often face significant computational limitations when dealing with intricate biological systems. This limitation stems from the exponential growth of computational complexity with increasing system size and interaction density. The proposed solution involves representing biological systems as graphs, where nodes represent individual biological entities (e.g., genes, proteins, cells, organisms) and edges represent the interactions between them. This graph representation allows for the application of efficient graph algorithms and simulation techniques, dramatically reducing computational burden. We detail the methodology, including graph construction, node and edge attributes, and simulation algorithms tailored for biological systems. The approach demonstrates scalability and offers a viable alternative for modeling complex biological interactions, particularly those involving large numbers of components and intricate feedback loops. We explore various simulation techniques applicable within this framework, such as random walks, message passing, and network diffusion, and discuss their suitability for different biological scenarios. The results, while hypothetical due to the absence of experimental data, illustrate the potential of this method for generating insights into system dynamics and identifying key regulatory pathways. The ultimate goal is to provide a robust and scalable platform for understanding the behavior of complex biological systems.
This paper describes the formulation of a numerical model for simulating environmentally driven one-dimensional (1D) ground movements of expansive clay. The formulation is based on a finite-element model that simulates the redistribution of matric suction through a diffusion-type equation, explicitly accounting for volume changes due to wetting and drying of the clay. We synthesize and modify highly nonlinear constitutive relationships for (1) hysteretic soil water retention; (2) reversible soil shrinkage and expansion of clay; and (3) hydraulic conductivity, explicitly incorporating desiccation cracks through a multidomain framework and assuming a critical surface crack depth. These models are well-calibrated to published laboratory tests on a reference expansive clay, Denver bentonite. We demonstrate capabilities of the proposed formulation to simulate the response of a homogeneous expansive clay to periods of drying and wetting, considering the initial matric suction, saturated hydraulic conductivity of the intact clay, and critical crack depth as three primary sources of uncertainty. We compare ensemble model simulations with measured ground movements from an instrumented expansive clay test site in Texas over a 3-year period using detailed records of potential evapotranspiration and precipitation. By assigning weights to the ensemble simulations based on their performance, we constrain the ranges of the three key uncertain parameters. The results showed very reasonable first-order agreement with the measured data and highlight the potential of the proposed formulation. We anticipate that more reliable predictions can be achieved through direct measurements of actual in situ evaporation rates and local soil properties.
Mahdi Seyyedan, Jiali Ma, Ivo Rosa Montenegro et al.· Journal of Geotechnical and...· 1 citation
A rational design for next-generation thermo-responsive nanocarriers is proposed, in which polymer chemistry, nanoparticle structure, experimental characterization, and mechanistic modelling are integrated from the earliest stages of material development.
M. Schifone, Giuseppe Nunziata, Filippo Rossi· Advances in Colloid and Inte...· 1 citation
This paper develops the economics of artificial intelligence as a single connected structure, from the physics of the production function to the aggregate growth constraint and the valuation of the firms building and adopting it. Part I derives the cost of capability from scaling laws, shows why deployed models are systematically overtrained, and estimates the task-success slope directly from 23,235 public evaluation runs: $\hat\beta=0.83$ with no detectable release-date trend. Part II treats market structure: minimum efficient scale, the two-tier equilibrium in which open weights contest the trailing edge but never the frontier, and inference as a capacity-constrained short-run market that rations rather than prices. Part III is the core. We replace the standard automation assignment rule with one that prices reliability, obtaining an automation calendar $t_{\mathrm{aut}}=t_{1/2}+(\tau/\beta)\log_2\gamma$ in which verification cost, not task difficulty, sets the date; derive optimal checkpoint spacing $k^\star\approx\sqrt{v_{\mathrm{ver}}/\lambda}$; and prove the exact best-of-$k$ result. Against a sound verifier, sampling divides the reliability lag by $k$ in the small-$k$ regime and does better outside it; against an unsound verifier, it leaves an error floor that no amount of sampling removes. Part IV aggregates: diffusion inherits its time dispersion from verification costs, and revenue growth is governed by the density of tasks at the current threshold. Part V proves a Baumol bound --- with elasticity of substitution below one, aggregate growth converges to that of the least automatable essential input --- and states three jointly necessary conditions for explosive growth. Part VI treats measurement, policy, and financial markets. Part VII states the investment bridge: technological importance, industry profit, and security return are distinct objects, and a coherent valuation must respect the automation calendar, rent migration, capital consumption, and expectations already in price. The full valuation architecture is reserved for a separate companion paper. Part VIII states eighteen open problems.
Miquel Noguer Alonso· Zenodo (CERN European Organi...· 0 citations
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.