Related papers: Kinetic limitations of cooperativity based drug de…
The molecular photo cell, i.e., a single molecule donor-acceptor complex, beside being technologically important, is a paradigmatic example of a many-body system operating in strong non-equilibrium. The quantum transport and the…
We model the mechanics of associating trivalent dendrimer network glasses with a focus on their energy dissipation properties. Various combinations of sticky bond (SB) strength and kinetics are employed. The toughness (work-to-fracture) of…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. We…
Modeling cell interactions such as co-attraction and contact-inhibition of locomotion is essential for understanding collective cell migration. Here, we propose a novel deep reinforcement learning model for collective neural crest cell…
Collective cell flows are a hallmark of tissue dynamics in development, wound healing, and various diseases. Here, we perform experiments on epithelial MDCK cell monolayers, over tens of hours without jamming, on millimeter-scale…
In order to study the effect of cell elastic properties on the behavior of assemblies of motile cells, this paper describes an alternative to the cell phase field (CPF) \cite{Palmieri2015} we have previously proposed. The CPF is a…
Our published and new experimental results by means of deuteron NMR spectroscopy in studies of molecular mobility in confinement are summarized and annalysed. Conclusions about limits of applicability of methods in disclosing several…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
The effect of structural constriction on molecular mobility is investigated by broadband dielectric spectroscopy (BDS) within three types of molecular arrangements: monomers, oligomers and self-assembled monolayers (SAMs). While disordered…
Molecular machines are stochastic systems that catalyze the energetic processes keeping living cells alive and structured. Inspired by the examples of F1-ATP synthase and the bacterial flagellum, we present a minimal model of an externally…
The mutations of a complex systemic disease like cancer can be modeled as stuck-at faults in the Boolean system paradigm. For a class of multiple faults, the fault identification is exceptionally significant under the incomplete access of…
Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly understood. Here we analyze distinct cellular networks…
Diffusive motion of regulatory enzymes on biopolymers with eventual capture at a reaction site is a common feature in cell biology. Using a lattice gas model we study the impact of diffusion and capture for a microtubule polymerase and a…
The study of the interactions of living adherent cells with mechanically stable (visco)elastic materials enables understanding and exploiting physiological phenomena mediated by cell-extracellular communication. However, insight on the…
Molecules with complex internal structure in time-dependent periodic potentials are studied by using short Rubinstein-Duke model polymers as an example. We extend our earlier work on transport in stochastically varying potentials to cover…
Evolutionary algorithms have long been used for optimization problems where the appropriate size of solutions is unclear a priori. The applicability of this methodology is here investigated on the problem of designing a nano-particle (NP)…
In this paper, the error performance achieved by cooperative detection among K distributed receivers in a diffusion-based molecular communication (MC) system is analyzed and optimized. In this system, the receivers first make local hard…
Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here we surprisingly observed that knotting can be very effectively produced in active polymers.…
We study the differences in electrical charge transport dynamics of the conductivity enhancement of poly(3,4-ethylenedioxythiophene) (PEDOT) derivatives under geometrical confinement. The results of polymer blend poly(3,4-ethylene…