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The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus,…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
Intercellular signaling has an important role in organism development, but not all communication occurs using the same mechanism. Here, we analyze the energy efficiency of intercellular signaling by two canonical mechanisms: diffusion of…
In this paper, we study the performance of detectors in a diffusive molecular communication environment where steady uniform flow is present. We derive the expected number of information molecules to be observed in a passive spherical…
Colloids coupled to a bath of swimming cells generically display enhanced diffusion. This transport dynamics stems from a subtle interplay between the active and passive particles that still resists our understanding despite decades of…
Microbial communities play a significant role in bioremediation,plant growth,human and animal digestion,global elemental cycles including the carbon-cycle,and water treatment.They are also posed to be the engines of renewable energy via…
Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
In diffusion-based molecular communication, information is transferred from a transmitter to a receiver using molecular carriers. The low achievable data rate is the main disadvantage of diffusion-based molecular over radio-based…
In a diffusion-based molecular communication network, transmitters and receivers communicate by using signalling molecules (or ligands) in a fluid medium. This paper assumes that the transmitter uses different chemical reactions to generate…
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…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Among the main actors of organism development there are morphogens, which are signaling molecules diffusing in the developing organism and acting on cells to produce local responses. Growth is thus determined by the distribution of such…
A simple manner to describe the diffusive relaxation of a colloidal fluid adsorbed in a porous medium is to model the porous medium as a set of spherical particles fixed in space at random positions with prescribed statistical structural…
How many times a diffusing molecule can permeate across a membrane or be adsorbed on a substrate? We employ the encounter-based approach to find the statistics of adsorption or permeation events for molecular diffusion in a general…
Rogue waves are intense and unexpected wavepackets ubiquitous in complex systems. In optics, they are promising as robust and noise-resistant beams for probing and manipulating the underlying material. Localizing large optical power is…
Understanding how colloids move in crowded environments is key for gaining control over their transport in applications such as drug delivery, filtration, contaminant/microplastic remediation and agriculture. The classical models of colloid…
Epidemic spreading often occurs in spatially heterogeneous environments, yet how quenched heterogeneity reshapes its onset and critical dynamics remains poorly understood. The diffusive epidemic process, a minimal reaction-diffusion model…
Originating from the diffusion phenomenon in physics, which describes the random movement and collisions of particles, diffusion generative models simulate a random walk in the data space along the denoising trajectory. This allows…