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Computational methods in drug repositioning can help to conserve resources. In particular, methods based on biological networks are showing promise. Considering only the network topology and knowledge on drug target genes is not sufficient…

Molecular Networks · Quantitative Biology 2025-04-02 Atte Aalto , La Mi , Diego A. Blanco-Mora , Jorge Goncalves

With increasing interest in adaptive clinical trial designs, challenges are present to drug supply chain management which may offset the benefit of adaptive designs. Thus, it is necessary to develop an optimization tool to facilitate the…

Applications · Statistics 2023-10-16 Jincheng Pang , Hong Yan , Zoe Hua

We recast the problem of hydrogel swelling under physical constraints as an energy optimization problem. We apply this approach to compute equilibrium shapes of hydrogel spheres confined within a jammed matrix of rigid beads, and interpret…

Soft Condensed Matter · Physics 2023-04-11 Chaitanya Joshi , Mathew Q. Giso , Jean-François Louf , Sujit S. Datta , Timothy J. Atherton

We study optimal control of diffusions with slow and fast variables and address a question raised by practitioners: is it possible to first eliminate the fast variables before solving the optimal control problem and then use the optimal…

Optimization and Control · Mathematics 2014-06-16 Wei Zhang , Juan C. Latorre , Grigorios A. Pavliotis , Carsten Hartmann

The dynamical response of an aircraft subject to gust perturbations is a key element in a preliminary design phase. In particular, the loads induced by gusts along the wing should not exceed some limit values and should even ideally be…

Systems and Control · Electrical Eng. & Systems 2021-07-05 Pierre Vuillemin , David Quero Martin , Charles Poussot-Vassal

The accuracy of meshless methods like Smoothed Particle Hydrodynamics (SPH) is highly dependent on the quality of the particle distribution. Existing particle initialization techniques often struggle to simultaneously achieve adaptive…

Computational Physics · Physics 2026-01-01 Navaneet Villodi , Prabhu Ramachandran

Theoretical approaches are formulated to investigate the molecular mobility under various cooling rates of amorphous drugs. We describe the structural relaxation of a tagged molecule as a coupled process of cage-scale dynamics and…

Soft Condensed Matter · Physics 2019-12-10 Anh D. Phan , Katsunori Wakabayashi , Marian Paluch , Vu D. Lam

Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…

Optimization and Control · Mathematics 2020-08-14 Amir Akbari , Bernhard O. Palsson

Control of the swelling, chemical functionalization, and adhesivity of hydrogels are finding new applications in a wide range of material systems. We investigate experimentally the effect of adsorbed particles on hydrogels on the depinning…

Soft Condensed Matter · Physics 2016-06-14 François Boulogne , François Ingremeau , Laurent Limat , Howard A. Stone

Organisms have evolved a variety of mechanisms to cope with the unpredictability of environmental conditions, and yet mainstream models of metabolic regulation are typically based on strict optimality principles that do not account for…

Molecular Networks · Quantitative Biology 2020-07-08 David S. Tourigny

The atomisation of suspension containing liquid and dispersed particles is prevalent in many applications. Previous studies of droplet breakup mainly focused on homogeneous fluids, and the heterogeneous effect of particles on the breakup…

Fluid Dynamics · Physics 2024-03-19 Zhikun Xu , Tianyou Wang , Zhizhao Che

One common approach for dose optimization is a two-stage design, which initially conducts dose escalation to identify the maximum tolerated dose (MTD), followed by a randomization stage where patients are assigned to two or more doses to…

Methodology · Statistics 2024-11-11 Yixuan Zhao , Rachael Liu , Jianchang Lin , Ying Yuan

In this paper, we discuss our recent works on the null-controllability, the exact controllability, and the stabilization of linear hyperbolic systems in one dimensional space using boundary controls on one side for the optimal time. Under…

Optimization and Control · Mathematics 2020-12-11 Jean-Michel Coron , Hoai-Minh Nguyen

Swelling is a volumetric-growth process in which a porous material expands by spontaneous imbibition of additional pore fluid. Swelling is distinct from other growth processes in that it is inherently poromechanical: Local expansion of the…

Soft Condensed Matter · Physics 2025-05-13 Thibault Bertrand , Jorge Peixinho , Shomeek Mukhopadhyay , Christopher W. MacMinn

We consider the bilinear optimal control of an advection-reaction-diffusion system, where the control arises as the velocity field in the advection term. Such a problem is generally challenging from both theoretical analysis and algorithmic…

Optimization and Control · Mathematics 2021-01-08 Roland Glowinski , Yongcun Song , Xiaoming Yuan , Hangrui Yue

This paper investigates the robustness of stochastic optimal control for controlled regime switching diffusions. We consider systems driven by both continuous fluctuations and discrete regime changes, allowing for model misspecification in…

Optimization and Control · Mathematics 2025-11-24 Somnath Pradhan , Dinesh Rathia

Effective disease treatment often requires precise control of the release of the active pharmaceutical ingredient (API). In this work, we present a computational inverse design approach to determine the optimal drug composition that yields…

Computational Engineering, Finance, and Science · Computer Science 2025-07-23 Rabia Altunay , Jarkko Suuronen , Eero Immonen , Lassi Roininen , Jari Hämäläinen

In this work we address the question of whether a low-density system composed of identical rough particles may reach hydrodynamic states (also called \textit{normal} states), even if energy is not conserved in particle collisions. As a way…

Soft Condensed Matter · Physics 2018-09-10 Francisco Vega Reyes , Andrés Santos , Gilberto M. Kremer

Estimating the reachable set of a dynamical system is a fundamental problem in control theory, particularly when control inputs are bounded. Direct simulation using randomly sampled admissible controls often leads to trajectories that…

Optimization and Control · Mathematics 2025-11-20 Karthik Elamvazhuthi , Sachin Shivakumar

Electroporation is a very useful tool for drug delivery into various diseased tissues of the human body. This technique helps to improve the clinical treatment by transferring drugs into the targeted cells rapidly. In electroporation, drug…

Functional Analysis · Mathematics 2022-08-03 Nilay Mondal , D. C. Dalal