Related papers: bcd mRNA active transport: 3D agent-based modeling
To help facilitate a variety of simulations related to healthcare facilities in North Carolina, we have developed an agent-based model (ABM) to accurately simulate patient (i.e., agent) movement to and from these facilities. This is an…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…
The concentration gradient of the Bicoid morphogen, which is established during the early stages of a Drosophila melanogaster embryonic development, determines the differential spatial patterns of gene expression and subsequent cell fate…
In this work, we present a new method for predicting bioaccumulation factor of organic molecules. The approach utilizes 3D convolutional neural network (ActivNet4) that uses solvent spatial distributions around solutes as input. These…
Generative agents offer promising capabilities for simulating realistic urban behaviors. However, existing methods oversimplify transportation choices, rely heavily on static agent profiles leading to behavioral homogenization, and inherit…
Machine learning approaches to Structure-Based Drug Design (SBDD) have proven quite fertile over the last few years. In particular, diffusion-based approaches to SBDD have shown great promise. We present a technique which expands on this…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
We present a distributed formation control strategy for agents with a variety of dynamics to achieve a desired planar formation. Our approach is based on the barycentric-coordinate-based (BCB) control, which is fully distributed, does not…
This article proposes a methodology to model and simulate complex systems, based on IRM4MLS, a generic agent-based meta-model able to deal with multi-level systems. This methodology permits the engineering of dynamic multi-level agent-based…
Most traffic flow control algorithms address switching cycle adaptation of traffic signals and lights. This work addresses traffic flow optimisation by self-organising micro-level control combining Reinforcement Learning and rule-based…
Experimental evidence suggests that epidermal growth factor receptor (EGFR)-mediated activation of the signaling protein phospholipase C gamma plays a critical role in a cancer cell's phenotypic decision to either proliferate or to migrate…
The potential power provided and possibilities presented by computation graphs has steered most of the available modeling techniques to re-implementing, utilization and including the complex nature of System Biology (SB). To model the…
We design 3D-printed motor-driven active particles and find that their dynamics can be characterized using the model of overdamped chiral active Brownian particles (ABPs), as demonstrated by measured angular statistics and translational…
Recent advances in diffusion models have demonstrated their strong capabilities in generating high-fidelity samples from complex distributions through an iterative refinement process. Despite the empirical success of diffusion models in…
In several network problems the optimum behavior of the agents (i.e., the nodes of the network) is not known before deployment. Furthermore, the agents might be required to adapt, i.e. change their behavior based on the environment…
This paper presents a software platform, named BiNS2, able to simulate diffusion-based molecular communications with drift inside blood vessels. The contribution of the paper is twofold. First a detailed description of the simulator is…
Individual traffic significantly contributes to climate change and environmental degradation. Therefore, innovation in sustainable mobility is gaining importance as it helps to reduce environmental pollution. However, effects of new ideas…
The predetermination, formation and maintenance of the primary morphogenetic gradient (bicoid gradient) of the early Drosophila embryo involves many interrelated processes. Here we focus on a system-biological analysis of the processes of…
Existing traffic simulation models often fall short in capturing the intricacies of real-world scenarios, particularly the interactive behaviors among multiple traffic participants, thereby limiting their utility in the evaluation and…
The wind-tunnel experiment plays a critical role in the design and development phases of modern aircraft, which is limited by prohibitive cost. In contrast, numerical simulation, as an important alternative paradigm, mimics complex flow…